diff --git a/.github/workflows/r_package_dev-nf.yaml b/.github/workflows/workflow_master.yaml similarity index 84% rename from .github/workflows/r_package_dev-nf.yaml rename to .github/workflows/workflow_master.yaml index ed3a1e2..a61a889 100644 --- a/.github/workflows/r_package_dev-nf.yaml +++ b/.github/workflows/workflow_master.yaml @@ -3,7 +3,8 @@ name: R GitHub Actions dev-nf on: push: branches: - - dev-nf + - master + - nfancy-patch-1 jobs: R-CMD-check: @@ -35,10 +36,7 @@ jobs: load: true file: ./Dockerfile tags: | - nfancy/scflow:${{ env.packageVersion }} nfancy/scflow:latest - nfancy/scflow:dev - - name: Login to DockerHub @@ -49,6 +47,4 @@ jobs: - name: push service run: | - docker push nfancy/scflow:${{ env.packageVersion }} docker push nfancy/scflow:latest - docker push nfancy/scflow:dev diff --git a/DESCRIPTION b/DESCRIPTION index 5f7fa3d..4ebad49 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: scFlow Title: A Single-Cell/Nuclei Analysis Toolkit -Version: 0.7.2 +Version: 0.7.4 Authors@R: c( person(given = "Combiz", @@ -41,21 +41,21 @@ Suggests: spelling, covr, knitr, - scFlowExamples, BiocStyle, DT (>= 0.26) Language: en-US -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 biocViews: Imports: + Matrix, assertthat (>= 0.2.1), bib2df, biomaRt (>= 2.54.0), cli (>= 3.4.1), cowplot (>= 1.1.1), DirichletReg (>= 0.7.1), - DoubletFinder (>= 2.0.3), dplyr (>= 1.1.0), + DoubletFinder (>= 2.0.3), DropletUtils (>= 1.18.1), edgeR (>= 3.40.0), english (>= 1.2.6), @@ -75,7 +75,7 @@ Imports: limma (>= 3.54.0), magrittr (>= 2.0.3), MAST (>= 1.24.0), - Matrix, + lme4, methods, monocle3 (>= 1.3.1), paletteer (>= 1.5.0), @@ -106,16 +106,11 @@ Imports: uwot, WebGestaltR Remotes: + NathanSkene/EWCE, chris-mcginnis-ucsf/DoubletFinder, ropensci/plotly, cole-trapnell-lab/monocle3, theislab/kBET, jlmelville/uwot, - NathanSkene/One2One, - hhoeflin/hdf5r, - mojaveazure/loomR, - neurogenomics/scFlowExamples, - ropensci/bib2df, - bzhanglab/WebGestaltR, - cran/riverplot + ropensci/bib2df VignetteBuilder: knitr diff --git a/Dockerfile b/Dockerfile index 2517673..fd15098 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,8 +1,8 @@ #LABEL maintainer="Combiz Khozoie, Ph.D. c.khozoie@imperial.ac.uk, Alan Murphy, a.murphy@imperial.ac.uk" ## Use rstudio installs binaries from RStudio's RSPM service by default, -## Uses the latest stable ubuntu, R and Bioconductor versions. Created on unbuntu 20.04, R 4.0 and BiocManager 3.12 -FROM rocker/rstudio:4.2.2 +## Uses the latest stable ubuntu, R and Bioconductor versions. Created on unbuntu 20.04, R 4.3 and BiocManager 3.18 +FROM rocker/rstudio:4.3 ## Add packages dependencies @@ -38,7 +38,7 @@ RUN apt-get update \ libcairo2-dev \ libtiff5-dev \ libreadline-dev \ - libgsl0-dev \ + libgsl-dev \ libgslcblas0 \ libgtk2.0-dev \ libgl1-mesa-dev \ @@ -111,7 +111,8 @@ RUN pip install stratocumulus \ && rm -rf /tmp/* -RUN install2.r -e \ +RUN install2.r -e -t source \ +Matrix \ argparse \ assertthat \ BiocManager \ @@ -138,12 +139,11 @@ ggridges \ Hmisc \ httr \ ids \ -igraph \ knitr \ leaflet \ -lme4 \ magrittr \ -Matrix \ +lme4 \ +igraph \ paletteer \ patchwork \ plyr \ @@ -166,6 +166,7 @@ Rtsne \ scales \ sctransform \ Seurat \ +SeuratObject \ snow \ spelling \ stringr \ @@ -178,6 +179,8 @@ tidyverse \ UpSetR \ utils \ vroom \ +WebGestaltR \ +apcluster \ && rm -rf /tmp/downloaded_packages ## Install Bioconductor packages @@ -187,18 +190,15 @@ RUN Rscript -e 'requireNamespace("BiocManager"); BiocManager::install(ask=F);' \ && rm -rf /tmp/downloaded_packages ## Install from GH the following -RUN installGithub.r chris-mcginnis-ucsf/DoubletFinder \ +RUN installGithub.r NathanSkene/EWCE \ +chris-mcginnis-ucsf/DoubletFinder \ ropensci/plotly \ cole-trapnell-lab/monocle3 \ theislab/kBET \ jlmelville/uwot \ -NathanSkene/One2One \ hhoeflin/hdf5r \ -mojaveazure/loomR \ ropensci/bib2df \ cvarrichio/Matrix.utils \ -neurogenomics/scFlowExamples \ -bzhanglab/WebGestaltR \ && rm -rf /tmp/downloaded_packages ## Install scFlow package diff --git a/NEWS.md b/NEWS.md index 5498076..d176425 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# scFlow 0.7.4 + +* Updated DoubletFinder version compatibility. +* Minor bug fixes in `map_celltypes_sce()`. The subsampling is now done per cluster to avoid smaller clusters being excluded. +* Change the order of the contrast vs reference names in DEG table. + # scFlow 0.7.2 * QC bug fixes. diff --git a/R/cluster_sce.R b/R/cluster_sce.R index 83147bb..12f1488 100644 --- a/R/cluster_sce.R +++ b/R/cluster_sce.R @@ -2,8 +2,16 @@ #' Cluster SingleCellExperiment with monocle3::cluster_cells #' #' @param sce a SingleCellExperiment object -#' @param ... see uwot::umap for umap options. Includes reduction_methods one -#' or more of "PCA", "tSNE", "UMAP", "UMAP3D" +#' @param cluster_method Available methods include leiden and louvain. +#' @param reduction_method Input slot for clustering. Available options are PCA, +#' UMAP_Liger, tSNE_Liger. +#' @param resolution Clustering resolution. If NULL, clustering method will be +#' set to louvain. +#' @param K Integer number of nearest neighbors to use when creating the k +#' nearest neighbor graph for Louvain/Leiden clustering. +#' k is related to the resolution of the clustering result, a bigger k will +#' result in lower resolution and vice versa. Default is 50. +#' @param ... see monocle3::cluster_cells for more clustering options. #' #' @return sce a SingleCellExperiment object annotated with reducedDims #' @@ -14,15 +22,22 @@ #' #' @export -cluster_sce <- function(sce, ...) { +cluster_sce <- function(sce, + cluster_method = "leiden", + reduction_method = "UMAP_Liger", + resolution = 1e-5, + k = 50, + louvain_iter = 1, + verbose = T, + ...) { fargs <- list( - cluster_method = "leiden", - reduction_method = "UMAP_Liger", - resolution = 1e-5, - k = 100, - louvain_iter = 1, - verbose = T + cluster_method = cluster_method, + reduction_method = reduction_method, + resolution = resolution, + k = k, + louvain_iter = louvain_iter, + verbose = verbose ) inargs <- list(...) diff --git a/R/diffexp_models.R b/R/diffexp_models.R index fe07fce..c7df829 100644 --- a/R/diffexp_models.R +++ b/R/diffexp_models.R @@ -413,7 +413,7 @@ perform_de <- function(sce, by = "ensembl_gene_id") } - element_name <- paste(fargs$ref_class, ctrast, sep = "_vs_") + element_name <- paste(ctrast, fargs$ref_class, sep = "_vs_") de_params <- list( celltype = unique(fargs$sce$cluster_celltype), diff --git a/R/integrate_sce.R b/R/integrate_sce.R index ad06362..4c12536 100644 --- a/R/integrate_sce.R +++ b/R/integrate_sce.R @@ -4,9 +4,9 @@ #' Produces a reducedDim slot representing common factors across datasets #' #' @param sce a SingleCellExperiment object or merged sce objects -#' @param method the integration method to use -#' Set to k=30 as default. -#' @param ... Additional arguments. Such as k Inner dimension of factorization +#' @param method the integration method to use. Set to liger as default. +#' See `liger_preprocess` and `liger_reduce_dims` functions for parameter options. +#' @param ... Additional arguments. Such as k, inner dimension of factorization #' (number of factors). #' #' @return sce SingleCellExperiment object annotated with reducedDims diff --git a/R/map_with_ewce.R b/R/map_with_ewce.R index b7bbe6c..133db3f 100644 --- a/R/map_with_ewce.R +++ b/R/map_with_ewce.R @@ -94,10 +94,20 @@ map_celltypes_sce <- function(sce, l_ctd <- .read_rds_files_to_list(ctd_folder) - if (dim(sce)[[2]] > cells_to_sample) { + + if(!is.null(cells_to_sample)){ + set.seed(123) + idx <- c() + for(i in as.character(unique(sce[[clusters_colname]]))){ + idx_temp <- which( sce[[clusters_colname]] == i) %>% + sample(size = min(cells_to_sample, length(.)), replace = FALSE ) + idx_temp <- idx_temp[order(idx_temp)] + idx <- c(idx, idx_temp)} + message(sprintf("Subsetting %s cells", cells_to_sample)) - set.seed(42) - sce_subset <- sce[, sample(dim(sce)[[2]], cells_to_sample)] + + sce_subset <- sce[, idx] + } else { sce_subset <- sce } diff --git a/README.Rmd b/README.Rmd index 459d917..e922e7f 100644 --- a/README.Rmd +++ b/README.Rmd @@ -90,6 +90,23 @@ You can install the development version of scFlow from GitHub with: - devtools::install_github("neurogenomics/scFlow") ``` +## Running RStudio Server with pre-installed scFlow via Docker + +If using linux system, open a cmd terminal and run the following commands: + +```{r eval = FALSE} +docker pull nfancy/scflow + +docker run --rm -d \ +-v $HOME:/home/rstudio/home \ +-e ROOT=true \ +-e PASSWORD=password \ +-p 8950:8787 \ +nfancy/scflow +``` + +Then access the RStudio Server on your browser at IP:8950. The default username is `rstudio` and password is `password`. To understand more on how to run docker Rstudio follow the link [here](https://davetang.org/muse/2021/04/24/running-rstudio-server-with-docker/). + ## Support * Ask a question on Stack Overflow with the scFlow tag, we monitor this for new questions. diff --git a/README.md b/README.md index a853860..8a42433 100644 --- a/README.md +++ b/README.md @@ -115,6 +115,27 @@ You can install the development version of scFlow from GitHub with: - devtools::install_github("neurogenomics/scFlow") ``` +## Running RStudio Server with pre-installed scFlow via Docker + +If using linux system, open a cmd terminal and run the following +commands: + +``` r +docker pull nfancy/scflow + +docker run --rm -d \ +-v $HOME:/home/rstudio/home \ +-e ROOT=true \ +-e PASSWORD=password \ +-p 8950:8787 \ +nfancy/scflow +``` + +Then access the RStudio Server on your browser at IP:8950. The default +username is `rstudio` and password is `password`. To understand more on +how to run docker Rstudio follow the link +[here](https://davetang.org/muse/2021/04/24/running-rstudio-server-with-docker/). + ## Support - Ask a question on Stack Overflow with the scFlow tag, we monitor diff --git a/docs/404.html b/docs/404.html index 6ab689c..d5b31c4 100644 --- a/docs/404.html +++ b/docs/404.html @@ -39,7 +39,7 @@ scFlow - 0.7.2 + 0.7.4 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index f100685..071beb0 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ scFlow - 0.7.2 + 0.7.4 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index dc03be1..6d84330 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ scFlow - 0.7.2 + 0.7.4 @@ -50,7 +50,6 @@

GNU General Public License

-

Version 3, 29 June 2007
Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>

Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

@@ -69,7 +68,7 @@

Preamble

TERMS AND CONDITIONS

-

0. Definitions

+

0. Definitions

“This License” refers to version 3 of the GNU General Public License.

“Copyright” also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.

“The Program” refers to any copyrightable work licensed under this License. Each licensee is addressed as “you”. “Licensees” and “recipients” may be individuals or organizations.

@@ -80,7 +79,7 @@

0. DefinitionsAn interactive user interface displays “Appropriate Legal Notices” to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion.

-

1. Source Code

+

1. Source Code

The “source code” for a work means the preferred form of the work for making modifications to it. “Object code” means any non-source form of a work.

A “Standard Interface” means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language.

The “System Libraries” of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A “Major Component”, in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it.

@@ -89,23 +88,23 @@

1. Source CodeThe Corresponding Source for a work in source code form is that same work.

-

2. Basic Permissions

+

2. Basic Permissions

All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law.

You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you.

Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not allowed; section 10 makes it unnecessary.

- +

No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures.

When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work’s users, your or third parties’ legal rights to forbid circumvention of technological measures.

-

4. Conveying Verbatim Copies

+

4. Conveying Verbatim Copies

You may convey verbatim copies of the Program’s source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program.

You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection for a fee.

-

5. Conveying Modified Source Versions

+

5. Conveying Modified Source Versions

You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under the terms of section 4, provided that you also meet all of these conditions:

  • a) The work must carry prominent notices stating that you modified it, and giving a relevant date.
    • @@ -118,7 +117,7 @@

    5. Conveying Modified Source Ve

A compilation of a covered work with other separate and independent works, which are not by their nature extensions of the covered work, and which are not combined with it such as to form a larger program, in or on a volume of a storage or distribution medium, is called an “aggregate” if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation’s users beyond what the individual works permit. Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate.

-

6. Conveying Non-Source Forms

+

6. Conveying Non-Source Forms

You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways:

  • a) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange.
    • @@ -138,7 +137,7 @@

    6. Conveying Non-Source Forms -

    7. Additional Terms

    +

    7. Additional Terms

    “Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.

    When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.

    Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms:

    @@ -159,24 +158,24 @@

    7. Additional Terms -

    8. Termination

    +

    8. Termination

    You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).

    However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.

    Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.

    Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10.

-

9. Acceptance Not Required for Having Copies

+

9. Acceptance Not Required for Having Copies

You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.

-

10. Automatic Licensing of Downstream Recipients

+

10. Automatic Licensing of Downstream Recipients

Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.

An “entity transaction” is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party’s predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.

You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.

-

11. Patents

+

11. Patents

A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor’s “contributor version”.

A contributor’s “essential patent claims” are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.

Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor’s essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version.

@@ -187,30 +186,30 @@

11. Patents -

12. No Surrender of Others’ Freedom

+

12. No Surrender of Others’ Freedom

If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.

-

13. Use with the GNU Affero General Public License

+

13. Use with the GNU Affero General Public License

Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.

-

14. Revised Versions of this License

+

14. Revised Versions of this License

The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.

Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation.

If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy’s public statement of acceptance of a version permanently authorizes you to choose that version for the Program.

Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.

-

15. Disclaimer of Warranty

+

15. Disclaimer of Warranty

THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

-

16. Limitation of Liability

+

16. Limitation of Liability

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

-

17. Interpretation of Sections 15 and 16

+

17. Interpretation of Sections 15 and 16

If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.

END OF TERMS AND CONDITIONS

diff --git a/docs/articles/index.html b/docs/articles/index.html index bac0152..186f404 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ scFlow - 0.7.2 + 0.7.4

diff --git a/docs/articles/scFlow.html b/docs/articles/scFlow.html index 4871a6b..cb1bd90 100644 --- a/docs/articles/scFlow.html +++ b/docs/articles/scFlow.html @@ -41,7 +41,7 @@ scFlow - 0.7.2 + 0.7.4
@@ -74,20 +74,18 @@ - - - - -
+ + + + +

-scFlow - Single-cell/nuclei RNA-seq -analysis tools in R for a complete workflow

-

This vignette -was created by Nurun Fancy and Combiz Khozoie

+scFlow - Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow +

This vignette was created by Nurun Fancy and Combiz Khozoie

-

18 April, 2023

+

18 February, 2024

Source: vignettes/scFlow.Rmd @@ -110,19 +108,17 @@

18 April, 2023

Overview

-

The goal of scFlow is to provide tools in R to build a complete -analysis workflow for single-cell/nuclei RNA sequencing data.

+

The goal of scFlow is to provide tools in R to build a complete analysis workflow for single-cell/nuclei RNA sequencing data.

  • Quality control of gene-cell matrices

  • Filtering of matrices by counts and features

    • -

  • Filtering of mitochondrial genes and mitochondrial counts -thresholding

    • +

  • Filtering of mitochondrial genes and mitochondrial counts thresholding

  • Doublet and multiplet identification and removal with DoubletFinder

  • Rich QC metrics annotation with scater

    • +

  • Dataset integration with Liger

  • Dimensionality reduction and celltype identification

    • -

  • Louvain clustering, UMAP dimensionality reduction, and cluster -marker gene identification with monocle

    • -

  • Celltype annotation with EWCE and Liger

    • +

  • Louvain clustering, UMAP dimensionality reduction, and cluster marker gene identification with monocle3

    • +

  • Celltype annotation with EWCE

  • Cluster identity mapping against the Allen Human Brain Atlas

  • Differential gene expression implementations

  • Zero-inflated regression model with MAST

    • @@ -136,86 +132,74 @@

    Overview

    Violin plots for gene expression.

  • Pathway and gene enrichment plots

-

The package functions are designed to interface neatly with NextFlow for scalable and -containerized pipelines deployed locally, on high-performance computing -clusters, or in the cloud. An accompanying NextFlow pipeline is in the -works - TBA.

+

The package functions are designed to interface neatly with NextFlow for scalable and containerized pipelines deployed locally, on high-performance computing clusters, or in the cloud. An accompanying NextFlow pipeline is in the works - TBA.

-

Install the dataset repository +

Install the scFlow and dataset repository

-
devtools::install_github("neurogenomics/scFlowExamples")
-

For a detailed explanation on how scFlowExamples dataset -was generated, visit this link.

+

First, install a few dependencies that aren’t automatically installed:

+
+options(repos = "https://cran.r-project.org/", pkgType = "source")
+install.packages("Matrix")
+install.packages("irlba")
+install.packages("Seurat")
+install.packages("SeuratObject")
+install.packages("lme4")
+install.packages("apcluster")
+remotes::install_github("NathanSkene/EWCE")
+remotes::install_github("chris-mcginnis-ucsf/DoubletFinder")
+

Now, install the latest version of scFlow.

+
+remotes::install_github("neurogenomics/scFlow")
+

For a detailed explanation on how scFlowExamples dataset was generated, visit this link.

Running scFlow

-

The scFlow pipeline requires three main input: a folder -containing matrix.mtx.gz, features.tsv.gz, -barcodes.tsv.gz for individual samples, a SampleSheet.tsv -file which is a tab-separated-variable file with sample metadata and a -Manifest.txt file is a tab-separated-variable file with two columns: -key and filepath. Details of how to generate -the files is given in this page

-

The basic scFlow workflow for sample QC begins with the -import of the feature-barcode sparse matrix with -read_sparse_matrix. The metadata for the sample is then -imported from a sample sheet with read_metadata. A -SingleCellExperiment object is created from the matrix and the metadata -using generate_sce which is then annotated with both gene -and cell-level data using annotate_sce. We then filter the -SingleCellExperiment to select only cells and genes meeting our QC -criteria using filter_sce. We can then optionally find -singlets in our filtered SingleCellExperiment using -find_singlets before filtering them out again with -filter_sce. A complete QC report can then be generated -using report_qc_sce before saving the filtered and -quality-controlled SingleCellExperiment with write_sce.

+

The scFlow pipeline requires three main input: a folder containing matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz for individual samples, a SampleSheet.tsv file which is a tab-separated-variable file with sample metadata and a Manifest.txt file is a tab-separated-variable file with two columns: key and filepath. Details of how to generate the files is given in this page

+

The basic scFlow workflow for sample QC begins with the import of the feature-barcode sparse matrix with read_sparse_matrix. The metadata for the sample is then imported from a sample sheet with read_metadata. A SingleCellExperiment object is created from the matrix and the metadata using generate_sce which is then annotated with both gene and cell-level data using annotate_sce. We then filter the SingleCellExperiment to select only cells and genes meeting our QC criteria using filter_sce. We can then optionally find singlets in our filtered SingleCellExperiment using find_singlets before filtering them out again with filter_sce. A complete QC report can then be generated using report_qc_sce before saving the filtered and quality-controlled SingleCellExperiment with write_sce.

-

Step one - set up example data & import the matrix and -metadata +

Step one - set up example data & import the matrix and metadata

Call required packages for vignette:

-
+
 #vignette packages
+library(apcluster) #need to load before scFlow to avoid function clash
 library(scFlow)
-library(scFlowExamples)
 library(SingleCellExperiment)
 library(dplyr)

-
First we must get and format the data from
-scFlowExamples for the vignette:

-
+
First we must get and format the data from scFlowExamples for the vignette:

+
 #create temp directory to store data
 outputDir <- tempdir()
-# write data, manifest and samplesheet to directory - 
-scFlowExamples::write_data(dataset="indvExp_ds_4K", output_dir=outputDir)
-scFlowExamples::write_scflow_manifest(dataset="indvExp_ds_4K", output_dir=outputDir)
-scFlowExamples::write_scflow_samplesheet(dataset="indvExp_ds_4K", 
-                                          output_dir=outputDir)
+
 #stored inside tmp_Zeisel2015_scflow inside directory:
-list.files(paste0(outputDir,"/tmp_Zeisel2015_scflow"))
+destpath <- file.path(outputDir, "tmp_Zeisel2015_scflow.zip")
+download.file(url = "https://github.com/neurogenomics/scFlow/releases/download/0.7.2/tmp_Zeisel2015_scflow.zip", destfile = destpath)
+unzip(destpath, exdir = outputDir)
+unlink(destpath)
+list.files(file.path(outputDir,"tmp_Zeisel2015_scflow"))
 ## [1] "individual_1"    "individual_2"    "individual_3"    "individual_4"   
 ## [5] "individual_5"    "individual_6"    "Manifest.txt"    "SampleSheet.tsv"

 
Now we can create file paths to each:

-
+
 #get locations to necessary files
-matrix_fp <- paste0(outputDir,"/tmp_Zeisel2015_scflow","/individual_1")
-samplesheet_fp <- paste0(outputDir,"/tmp_Zeisel2015_scflow","/SampleSheet.tsv")
-manifest_fp <- paste0(outputDir,"/tmp_Zeisel2015_scflow","/Manifest.txt")
+matrix_fp <- file.path(outputDir,"tmp_Zeisel2015_scflow","individual_1")
+samplesheet_fp <- file.path(outputDir,"tmp_Zeisel2015_scflow","SampleSheet.tsv")
+manifest_fp <- file.path(outputDir,"tmp_Zeisel2015_scflow","Manifest.txt")
 #Also need mapping and ctd file which can be downloaded
 ensembl_fp <- file.path(outputDir, "ensembl_mappings.tsv")
-ctd_fp <- outputDir
-download.file(url = "https://raw.githubusercontent.com/combiz/scFlowData/dev-nf/assets/ensembl_mappings_human.tsv", destfile = ensembl_fp)
-download.file(url = "https://raw.githubusercontent.com/combiz/scFlowData/dev-nf/ctd/ctd_allAIBS.rds", destfile = file.path(ctd_fp, "ctd_allAIBS.rds"))

+download.file(url = "https://github.com/neurogenomics/scFlow/releases/download/0.7.2/ensembl_mappings_human.tsv", destfile = ensembl_fp)
+
+ctd_fp <- file.path(outputDir, "ctd_folder")
+dir.create(ctd_fp)
+download.file(url = "https://github.com/neurogenomics/scFlow/releases/download/0.7.2/ctd_AIBS_v2.rds", destfile = file.path(ctd_fp, "ctd_AIBS_v2.rds"))

 
To run scFlow, we first need to read in the data matrix:

-
-mat <- read_sparse_matrix(matrix_fp)

-
Next, we retrieve the metadata by pointing to a Sample Sheet and
-specifying a unique identifier (unique_key) in a specific column
-(key_colname):

 
+mat <- read_sparse_matrix(matrix_fp)

+
Next, we retrieve the metadata by pointing to a Sample Sheet and specifying a unique identifier (unique_key) in a specific column (key_colname):

+
 #get name generated for first row in case changes
 first_sample <- read.table(file = samplesheet_fp, 
                            sep = '\t', header = TRUE)[1,1]
@@ -226,21 +210,16 @@ 
Step one
 )
 ## 
 ## ── Reading sample metadata ─────────────────────────────────────────────────────
-## Reading /tmp/RtmpkBxDeH/tmp_Zeisel2015_scflow/SampleSheet.tsv  
+## Reading /tmp/RtmpWmQoYJ/tmp_Zeisel2015_scflow/SampleSheet.tsv  
 ## 
-## ✔ Five metadata variables loaded for manifest='hahop'
-## manifest: `hahop` (factor)
+## ✔ Five metadata variables loaded for manifest='majos'
+## manifest: `majos` (factor)
 ## individual: `1` (integer)
 ## diagnosis: `Cases` (factor)
-## sex: `M` (factor)
-## age: `3` (integer)

-
For downstream analyses it’s important that the variable classes are
-correctly specified. Carefully inspect the metadata classes in brackets.
-In the above example we see that the individual were imported
-as integer rather than factor variables. Let’s correct this by reloading
-the metadata, this time specifying the correct variable classes for this
-variable:-

-
+## sex: `F` (factor)
+## age: `15` (integer)

+
For downstream analyses it’s important that the variable classes are correctly specified. Carefully inspect the metadata classes in brackets. In the above example we see that the individual were imported as integer rather than factor variables. Let’s correct this by reloading the metadata, this time specifying the correct variable classes for this variable:-

+
 var_classes <- c(
   individual = "factor"
 )
@@ -251,100 +230,88 @@ 
Step one
   samplesheet_path = samplesheet_fp,
   col_classes = var_classes
 )
-## Reading /tmp/RtmpkBxDeH/tmp_Zeisel2015_scflow/SampleSheet.tsv  
+## Reading /tmp/RtmpWmQoYJ/tmp_Zeisel2015_scflow/SampleSheet.tsv  
 ## 

-
With the metadata imported with the correct variable classes, and the
-previously loaded sparse matrix, we can generate our
-SingleCellExperiment object:-

-
+
With the metadata imported with the correct variable classes, and the previously loaded sparse matrix, we can generate our SingleCellExperiment object:-

+
 sce <- generate_sce(mat, metadata)

-
The SingleCellExperiment object was succesfully created and we can
-now proceed with annotation.

+
The SingleCellExperiment object was succesfully created and we can now proceed with annotation.

 

 

-
Step two – Annotate the SingleCellExperiment
+
Step two – Modelling ambient RNA profiling and annotating the SingleCellExperiment
 

-
In scFlow we specify all of our QC preferences and
-cutoffs with the annotate_sce command. This will also
-produce plots in the sce@metadata slot allowing rapid
-revision and optimization of QC parameters. Lets start with the default
-parameters by simply providing the SingleCellExperiment
-object to the annotate_sce function:-

-
+
For snRNAseq data generated by 10X genomics, the initial mapping of the raw fastq files to the reference genome generates raw_feature_bc_matrix and filtered_feature_bc_matrix. Ambient RNA profiling is performed optionally on the raw_feature_bc_matrix using the EmptyDrops algorithm to flag and subsequently filter cellular barcodes which do not deviate from an ambient RNA expression profile representing cell-free transcripts. This step is optional and will only work when starting from raw_feature_bc_matrix files. We did not run this step.

+
+#Optional
+sce <- find_cells(
+  sce,
+  lower  = 100,
+  retain = "auto",
+  niters = 10000
+)

+
In scFlow we specify all of our QC preferences and cutoffs with the annotate_sce command. This will also produce plots in the sce@metadata slot allowing rapid revision and optimization of QC parameters. Lets start with the default parameters by simply providing the SingleCellExperiment object to the annotate_sce function:-

+
 sce <- annotate_sce(
   sce,
   ensembl_mapping_file = ensembl_fp
 )
 ## ══ Annotating SingleCellExperiment ═════════════════════════════════════════════ 
 ## ══ Annotating SingleCellExperiment genes ═══════════════════════════════════════ 
-## Reading /tmp/RtmpkBxDeH/ensembl_mappings.tsv  
+## Reading /tmp/RtmpWmQoYJ/ensembl_mappings.tsv  
 ## ── Annotating SingleCellExperiment cells ─────────────────────────────────────── 
 ## ══ Generating QC plots for SingleCellExperiment ════════════════════════════════ 

-
A list of QC plots are available to browse in the
-sce@metadata$qc_plots, e.g.

-
+
A list of QC plots are available to browse in the sce@metadata$qc_plots, e.g.

+
 sce@metadata$qc_plots$number_genes_vs_count_depth

-

-
After running annotate_sce we may examine the plots and
-assess whether the applied thresholds are sensible for the sample. The
-effects of different parameters can be explored by iterating through the
-above generate_sce and annotate_sce functions
-until satisfied with the settings.

-
The next step is to filter the SingleCellExperiment with
-filter_sce: -

-
+

+
After running annotate_sce we may examine the plots and assess whether the applied thresholds are sensible for the sample. The effects of different parameters can be explored by iterating through the above generate_sce and annotate_sce functions until satisfied with the settings.

+
The next step is to filter the SingleCellExperiment with filter_sce: -

+
 sce <- filter_sce(sce)
 ## ══ Filtering SingleCellExperiment ══════════════════════════════════════════════ 
-## Pre-filtered SingleCellExperiment contains 3636 genes and 226 cells.
-## ✔ 12/0 mitochondrial genes were dropped. 
-## ✔ 0/68 ribosomal genes were dropped. 
-## ✔ 50/50 unmapped genes were dropped. 
-## ✔ 262 non-expressive genes were dropped. 
-## ✔ 3313/3636 genes passed QC. 
-## ✔ 6 cells failed QC and were dropped: - 
-## Library size QC: PASS: 223/FAIL: 3
-## Number of genes QC: PASS: 226/FAIL: 0
-## Mitochondria counts proportion QC: PASS: 226/FAIL: 0
-## Ribosomal counts proportion QC: PASS: 226/FAIL: 0
-## Overall cell QC: PASS: 220/FAIL: 6
-## ✔ SingleCellExperiment was filtered successfully to 3313 genes and 220 cells. 

+## Pre-filtered SingleCellExperiment contains 15882 genes and 2188 cells.
+## ✔ 60/0 mitochondrial genes were dropped. 
+## ✔ 0/79 ribosomal genes were dropped. 
+## ✔ 280/280 unmapped genes were dropped. 
+## ✔ 7390 non-expressive genes were dropped. 
+## ✔ 8309/15882 genes passed QC. 
+## ✔ 44 cells failed QC and were dropped: - 
+## Library size QC: PASS: 2186/FAIL: 2
+## Number of genes QC: PASS: 2188/FAIL: 0
+## Mitochondria counts proportion QC: PASS: 2188/FAIL: 0
+## Ribosomal counts proportion QC: PASS: 2188/FAIL: 0
+## Overall cell QC: PASS: 2144/FAIL: 44
+## ✔ SingleCellExperiment was filtered successfully to 8309 genes and 2144 cells. 

 

 

 
Step three – Finding singlets and discarding multiplets
 

-
At this stage we may wish to identify singlets in the
-SingleCellExperiment and discard any multiplets. In
-scFlow we simply run find_singlets and specify
-our preferred multiplet identification algorithm. Here we will use
-doubletfinder (This will take a while depending on the cell
-numbers):-

-
+
At this stage we may wish to identify singlets in the SingleCellExperiment and discard any multiplets. In scFlow we simply run find_singlets and specify our preferred multiplet identification algorithm. Here we will use doubletfinder (This will take a while depending on the cell numbers):-

+
 sce <- find_singlets(sce, "doubletfinder", pK = 0.005, vars_to_regress_out = c("nCount_RNA", "pc_mito"))

-
Now we can filter out these multiplets with
-filter_sce:-

-
+
Now we can filter out these multiplets with filter_sce:-

+
 sce <- filter_sce(sce)

 
You can see the remaining cells after all the filtering done by:

-
+
 dim(sce)
-## [1] 3313  219

-
Finally we produce a report with report_qc_sce (this
-takes a few minutes): -

-
+## [1] 8309 2107

+
Finally we produce a report with report_qc_sce (this takes a few minutes): -

+
 #Store results in same temp dir
 report_qc_sce(sce, report_file = "qc_report_scflow_individual_1",
-              report_folder_path = paste0(outputDir,"/tmp_Zeisel2015_scflow/"))
+              report_folder_path = file.path(outputDir,"/tmp_Zeisel2015_scflow/"))
 ## ══ Generating QC report for SingleCellExperiment ═══════════════════════════════ 
 ## class: SingleCellExperiment 
-## dim: 3313 219 
+## dim: 8309 2107 
 ## metadata(8): metadata scflow_steps ... citations doubletfinder_params
 ## assays(1): counts
-## rownames(3313): ENSG00000000419 ENSG00000001461 ... ENSG00000278588
+## rownames(8309): ENSG00000000003 ENSG00000000419 ... ENSG00000285053
 ##   ENSG00000285441
 ## rowData names(13): ensembl_gene_id gene_biotype ...
 ##   qc_metric_is_expressive qc_metric_gene_passed
-## colnames(219): hahop_1_TEINH_2 hahop_1_TEINH_3 ... hahop_1_MOL1_225
-##   hahop_1_MOL1_226
+## colnames(2107): majos_Teinh_1 majos_Teinh_2 ... majos_MOL1_2187
+##   majos_MOL1_2188
 ## colData names(18): barcode manifest ... qc_metric_max_features
 ##   is_singlet
 ## reducedDimNames(3): pca_by_individual tsne_by_individual
@@ -352,37 +319,30 @@ 
Step three – Fi
 ## mainExpName: NULL
 ## altExpNames(0):

 
And save our SingleCellExperiment: -

-
+
 #create dir to hold resulting sce
-dir.create(paste0(outputDir,"/sce_individual_1"))
-write_sce(sce, folder_path=paste0(outputDir,"/sce_individual_1"))

+dir.create(file.path(outputDir,"/sce_individual_1"))
+write_sce(sce, folder_path= file.path(outputDir,"/sce_individual_1"))

 

 

-
Step four – Merging multiple datasets into one
-SingleCellExperiment object
+
Step four – Merging multiple datasets into one SingleCellExperiment object
 

-
Follow step one-three for all individual samples and save them using
-write_sce function. Then we read the individual
-SingleCellExperiment using read_sce into a
-list and merge them using merge_sce function. Begin by
-reading in the manifest and samplesheet and listing the file path to all
-individuals:

-
+
Follow step one-three for all individual samples and save them using write_sce function. Then we read the individual SingleCellExperiment using read_sce into a list and merge them using merge_sce function. Begin by reading in the manifest and samplesheet and listing the file path to all individuals:

+
 manifest <- read.delim(manifest_fp)
 samplesheet <- read.delim(samplesheet_fp)
 dir_list <- 
-  dir(path = paste0(outputDir,"/tmp_Zeisel2015_scflow"), 
+  dir(path = file.path(outputDir,"/tmp_Zeisel2015_scflow"), 
         pattern = "individual_[0-9]$", full.names = TRUE)
 dir_list
-## [1] "/tmp/RtmpkBxDeH/tmp_Zeisel2015_scflow/individual_1"
-## [2] "/tmp/RtmpkBxDeH/tmp_Zeisel2015_scflow/individual_2"
-## [3] "/tmp/RtmpkBxDeH/tmp_Zeisel2015_scflow/individual_3"
-## [4] "/tmp/RtmpkBxDeH/tmp_Zeisel2015_scflow/individual_4"
-## [5] "/tmp/RtmpkBxDeH/tmp_Zeisel2015_scflow/individual_5"
-## [6] "/tmp/RtmpkBxDeH/tmp_Zeisel2015_scflow/individual_6"

-
Now loop through each, performing the analysis and finally merging
-the results:

-
+## [1] "/tmp/RtmpWmQoYJ//tmp_Zeisel2015_scflow/individual_1"
+## [2] "/tmp/RtmpWmQoYJ//tmp_Zeisel2015_scflow/individual_2"
+## [3] "/tmp/RtmpWmQoYJ//tmp_Zeisel2015_scflow/individual_3"
+## [4] "/tmp/RtmpWmQoYJ//tmp_Zeisel2015_scflow/individual_4"
+## [5] "/tmp/RtmpWmQoYJ//tmp_Zeisel2015_scflow/individual_5"
+## [6] "/tmp/RtmpWmQoYJ//tmp_Zeisel2015_scflow/individual_6"

+
Now loop through each, performing the analysis and finally merging the results:

+
 sce_list <- list()
 
 for(i in dir_list){
@@ -411,14 +371,14 @@ 
= c("nCount_RNA", "pc_mito"), 
                         num.cores = 1)
   sce <- filter_sce(sce)
-  outdir <-paste0(outputDir,"/scflow_vignette_data")
+  outdir <- file.path(outputDir,"/scflow_vignette_data")
   dir.create(outdir, showWarnings = FALSE)
   
   dir_report <- file.path(outdir, "qc_report")
   dir.create(dir_report, showWarnings = FALSE)
   
-  report_qc_sce(sce, report_file = paste("qc_report_", basename(i), sep = ""),
-                report_folder_path = dir_report)
+  #report_qc_sce(sce, report_file = paste0("qc_report_", basename(i)),
+  #              report_folder_path = dir_report)
   
   sce_list[[basename(i)]] <- sce
   
@@ -428,12 +388,8 @@ 
sce_list,
   ensembl_mapping_file = ensembl_fp
 )

-
After merging individual sce objects we can annotate and
-get an interactive html report on the merged sce using
-annotate_merged_sce and report_merged_sce
-functions respectively. Then we write the merged
-SingleCellExperiment object.

-
+
After merging individual sce objects we can annotate and get an interactive html report on the merged sce using annotate_merged_sce and report_merged_sce functions respectively. Then we write the merged SingleCellExperiment object.

+
 final_sce <- file.path(outdir, "sce")
 dir.create(final_sce)
 #annotate and save sce
@@ -443,91 +399,55 @@ 
= TRUE)

 

 

-
Step five – Dataset integration, dimension reduction and
-clustering
+
Step five – Dataset integration, dimension reduction and clustering
 

-
Once we merge all the samples into one
-SingleCellExperiment object we can move to the next steps
-of integration, dimension reduction and clustering. We have implemented
-liger for
-integrating datasets from multiple samples, treatment and experiments.
-For optimal integration user should try to use different k values.

-
Once data integration is done, dimension reduction is performed using
-multiple methods by default i.e. “PCA”, “tSNE”, “UMAP”, “UMAP3D”. For
-tSNE and UMAP, dimension reduction is performed using either PCA or
-Liger values. Once the dimension reduction step is done the
-SingleCellExperiment object is ready for clustering.

-
+
Once we merge all the samples into one SingleCellExperiment object we can move to the next steps of integration, dimension reduction and clustering. We have implemented liger for integrating datasets from multiple samples, treatment and experiments. For optimal integration user should try to use different k values.

+
Once data integration is done, dimension reduction is performed using multiple methods by default i.e. “PCA”, “tSNE”, “UMAP”, “UMAP3D”. For tSNE and UMAP, dimension reduction is performed using either PCA or Liger values. Once the dimension reduction step is done the SingleCellExperiment object is ready for clustering.

+
 dim(sce)
-## [1] 3552 1321

-
+## [1]  9902 12438

+
 #sample genes and samples for speed
 sce <- integrate_sce(sce, method = "Liger", k = 20)
 sce <- reduce_dims_sce(sce, pca_dims = 5, reduction_methods = "UMAP")

-
We can now plot UMAP generated using liger valuses using the
-following command:-

-
+
We can now plot UMAP generated using liger valuses using the following command:-

+
 plot_reduced_dim(sce, feature_dim = "diagnosis", 
                  reduced_dim = "UMAP_Liger", alpha = 1, size = 1)

-

-
The next step is to cluster all the cells using
-cluster_sce command.

-
-sce <- cluster_sce(sce, reduction_method = "UMAP_Liger", pca_dims = 5, k = 50)

+

+
The next step is to cluster all the cells using cluster_sce command.

+
+sce <- cluster_sce(sce, reduction_method = "UMAP_Liger", pca_dims = 5, k = 50,
+                   resolution = NULL)

 
We can then plot the clusters:-

-
+
 plot_reduced_dim(sce, feature_dim = "clusters", 
                  reduced_dim = "UMAP_Liger", alpha = 1, size = 1)

-

-
The next step is to annotate the celltypes for each cluster. Here, we
-will use the package ewce. For this
-we use the following command (This may take a while). To know how the
-ctd was generated please visit EWCE package
-webpage. Users can generate and provide custom ctd. The
-annotation level can be an integer or a named list as shown in the
-code.

-
+

+
The next step is to annotate the celltypes for each cluster. Here, we will use the package ewce. For this we use the following command (This may take a while). To know how the ctd was generated please visit EWCE package webpage. Users can generate and provide custom ctd. The annotation level can be an integer or a named list as shown in the code.

+
 sce <- map_celltypes_sce(sce,
                          ctd_folder = ctd_fp, 
-                         annotation_level = list("ctd_allAIBS" = c(1,2)),
-                         label_index = 2)

-
The celltypes for each cell can be found in
-sce@colData$cluster_celltype slot. We can also generate
-UMAP_Liger plot for each celltype.

-
+                         annotation_level = list("ctd_AIBS_v2" = c(1,2)),
+                         label_index = 1)

+
The celltypes for each cell can be found in sce@colData$cluster_celltype slot. We can also generate UMAP_Liger plot for each celltype.

+
 plot_reduced_dim(sce, 
                  feature_dim = "cluster_celltype",
                  reduced_dim = "UMAP_Liger", 
                  alpha = 1,
                  size = 1)

-

-
Our pipeline generates multiple reports.
-report_integrated_sce generates a report on integration
-whereas report_celltype_metrics generates detailed metrics
-on cell type distribution. Before running
-report_integrated_sce and
-report_celltype_metrics, the user needs to run
-annotate_integrated_sce and
-annotate_celltype_metrics functions respectively.

+

+
Our pipeline generates multiple reports. report_integrated_sce generates a report on integration whereas report_celltype_metrics generates detailed metrics on cell type distribution. Before running report_integrated_sce and report_celltype_metrics, the user needs to run annotate_integrated_sce and annotate_celltype_metrics functions respectively.

 

 

-
Step six – Performing differential expression analysis following by
-impacted pathway analysis
+
Step six – Performing differential expression analysis following by impacted pathway analysis
 

-
We need to subset the merged SingleCellExperiment object
-to perform differential expression analysis. Here we are using
-MASTZLM for differential expression analysis. For example,
-we are interested in performing DE analysis in the Oligo
-cell cluster. So, we first subset the Oligo cluster.

-
+
We need to subset the merged SingleCellExperiment object to perform differential expression analysis. Here we are using MASTZLM for differential expression analysis. For example, we are interested in performing DE analysis in the Oligo cell cluster. So, we first subset the Oligo cluster.

+
 sce_subset <- sce[, sce$clusters == 1]

-
We need to specify the colData column name as dependent_var as the
-variable of interest for DE analysis. For example here we want to
-perform DE analysis between Case and Controls which is found in
-diagnosis column. ref_class is the reference group for DE
-analysis. If there are any confounding variables those colData names can
-be passed through confounding_vars argument.

-
+
We need to specify the colData column name as dependent_var as the variable of interest for DE analysis. For example here we want to perform DE analysis between Case and Controls which is found in diagnosis column. ref_class is the reference group for DE analysis. If there are any confounding variables those colData names can be passed through confounding_vars argument.

+
 result_de <- perform_de(
   sce_subset,
   mast_method = "glmer",
@@ -539,37 +459,31 @@ 
= "manifest",
   ensembl_mapping_file = ensembl_fp,
   nAGQ = 0)

-
result_de returns a list of DE tables based on how many contrast is
-being done in one celltype.

-
-DT::datatable(result_de$Controls_vs_diagnosisCases,
+
result_de returns a list of DE tables based on how many contrast is being done in one celltype.

+
+DT::datatable(result_de$diagnosisCases_vs_Controls,
               rownames = FALSE, 
               escape = FALSE,
               options = list(pageLength = 5, 
                              scrollX=T, 
                              autoWidth = TRUE,
                              dom = 'Blfrtip'))

-

-
We have implemented two different functional enrichment tools enrichR
-and WebGestaltR. Users can call both tools using
-find_impacted_pathway() function. Here we will use
-WebGestaltR only.

-
+

+
We have implemented two different functional enrichment tools enrichR and WebGestaltR. Users can call both tools using find_impacted_pathway() function. Here we will use enrichR only. A report can be generated on the output of the find_impacted_pathway() function using report_impacted_pathway().

+
 # Get the significant genes for impacted pathway analysis
 
-sig_de <- result_de$Controls_vs_diagnosisCases %>%
-  dplyr::filter(padj <= 0.05) %>%
+sig_de <- result_de$diagnosisCases_vs_Controls %>%
+  dplyr::filter(padj <= 0.05, abs(logFC) >= 1.5) %>%
   dplyr::pull(gene) %>%
   as.character()
 
-enrichment_result <- pathway_analysis_webgestaltr(sig_de,
-                                                  enrichment_method = "ORA")
-## Loading the functional categories...
-## Loading the ID list...
-## Loading the reference list...
-## Performing the enrichment analysis...

-
-DT::datatable(enrichment_result$geneontology_biological_process_noredundant,
+enrichment_result <- pathway_analysis_enrichr(
+  sig_de,
+  enrichment_database = c("GO_Biological_Process_2021", 
+                          "KEGG_2021_Human"))

+
+DT::datatable(enrichment_result$GO_Biological_Process_2021,
               rownames = FALSE, 
               escape = FALSE,
               options = list(pageLength = 5, 
@@ -577,23 +491,14 @@ 
= TRUE,
                              columnDefs = list(list(width = '500px', targets = 1)),
                              dom = 'Blfrtip'))

-

-
+

+
 

 

 
Step seven – Additional analysis
 

-
Single cell RNA seq data enables to study cell type composition in
-tissue and as a result we can perform a differential cell type
-composition analysis. We have implemented Dirichlet-multinomial
-regression analysis to compare cell type composition changes across a
-categorical dependent variables. model_celltype_freqs
-performs the differential composition analysis and generate plots. Here
-we will compare if there are any changes in the composition of cell
-types between Controls and Cases. Additional
-confounding variables can be passed via confounding_vars
-parameter.

-
+
Single cell RNA seq data enables to study cell type composition in tissue and as a result we can perform a differential cell type composition analysis. We have implemented Dirichlet-multinomial regression analysis to compare cell type composition changes across a categorical dependent variables. model_celltype_freqs performs the differential composition analysis and generate plots. Here we will compare if there are any changes in the composition of cell types between Controls and Cases. Additional confounding variables can be passed via confounding_vars parameter.

+
 results <- model_celltype_freqs(
   sce,
   unique_id_var = "manifest",
@@ -602,13 +507,11 @@ 
Step seven – Additional analysis  ref_class = "Controls",
   var_order = c("Controls", "Cases")
 )

-
``model_celltype_freq returns a list of plots and the pvalues from
-the analysis.

-
+
``model_celltype_freq returns a list of plots and the pvalues from the analysis.

+
 results$dirichlet_plot

-

-
The complete result can be viewed as a html report
-generated by the function report_celltype_model.

+

+
The complete result can be viewed as a html report generated by the function report_celltype_model.

 

   

 
diff --git a/docs/articles/scFlow_files/crosstalk-1.2.1/css/crosstalk.min.css b/docs/articles/scFlow_files/crosstalk-1.2.1/css/crosstalk.min.css
new file mode 100644
index 0000000..6b45382
--- /dev/null
+++ b/docs/articles/scFlow_files/crosstalk-1.2.1/css/crosstalk.min.css
@@ -0,0 +1 @@
+.container-fluid.crosstalk-bscols{margin-left:-30px;margin-right:-30px;white-space:normal}body>.container-fluid.crosstalk-bscols{margin-left:auto;margin-right:auto}.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column{display:inline-block;padding-right:12px;vertical-align:top}@media only screen and (max-width: 480px){.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column{display:block;padding-right:inherit}}.crosstalk-input{margin-bottom:15px}.crosstalk-input .control-label{margin-bottom:0;vertical-align:middle}.crosstalk-input input[type="checkbox"]{margin:4px 0 0;margin-top:1px;line-height:normal}.crosstalk-input .checkbox{position:relative;display:block;margin-top:10px;margin-bottom:10px}.crosstalk-input .checkbox>label{padding-left:20px;margin-bottom:0;font-weight:400;cursor:pointer}.crosstalk-input .checkbox input[type="checkbox"],.crosstalk-input .checkbox-inline input[type="checkbox"]{position:absolute;margin-top:2px;margin-left:-20px}.crosstalk-input .checkbox+.checkbox{margin-top:-5px}.crosstalk-input .checkbox-inline{position:relative;display:inline-block;padding-left:20px;margin-bottom:0;font-weight:400;vertical-align:middle;cursor:pointer}.crosstalk-input .checkbox-inline+.checkbox-inline{margin-top:0;margin-left:10px}
diff --git a/docs/articles/scFlow_files/crosstalk-1.2.1/js/crosstalk.js b/docs/articles/scFlow_files/crosstalk-1.2.1/js/crosstalk.js
new file mode 100644
index 0000000..fd9eb53
--- /dev/null
+++ b/docs/articles/scFlow_files/crosstalk-1.2.1/js/crosstalk.js
@@ -0,0 +1,1474 @@
+(function(){function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o b) {
+    return 1;
+  }
+}
+
+/**
+ * @private
+ */
+
+var FilterSet = function () {
+  function FilterSet() {
+    _classCallCheck(this, FilterSet);
+
+    this.reset();
+  }
+
+  _createClass(FilterSet, [{
+    key: "reset",
+    value: function reset() {
+      // Key: handle ID, Value: array of selected keys, or null
+      this._handles = {};
+      // Key: key string, Value: count of handles that include it
+      this._keys = {};
+      this._value = null;
+      this._activeHandles = 0;
+    }
+  }, {
+    key: "update",
+    value: function update(handleId, keys) {
+      if (keys !== null) {
+        keys = keys.slice(0); // clone before sorting
+        keys.sort(naturalComparator);
+      }
+
+      var _diffSortedLists = (0, _util.diffSortedLists)(this._handles[handleId], keys),
+          added = _diffSortedLists.added,
+          removed = _diffSortedLists.removed;
+
+      this._handles[handleId] = keys;
+
+      for (var i = 0; i < added.length; i++) {
+        this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;
+      }
+      for (var _i = 0; _i < removed.length; _i++) {
+        this._keys[removed[_i]]--;
+      }
+
+      this._updateValue(keys);
+    }
+
+    /**
+     * @param {string[]} keys Sorted array of strings that indicate
+     * a superset of possible keys.
+     * @private
+     */
+
+  }, {
+    key: "_updateValue",
+    value: function _updateValue() {
+      var keys = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : this._allKeys;
+
+      var handleCount = Object.keys(this._handles).length;
+      if (handleCount === 0) {
+        this._value = null;
+      } else {
+        this._value = [];
+        for (var i = 0; i < keys.length; i++) {
+          var count = this._keys[keys[i]];
+          if (count === handleCount) {
+            this._value.push(keys[i]);
+          }
+        }
+      }
+    }
+  }, {
+    key: "clear",
+    value: function clear(handleId) {
+      if (typeof this._handles[handleId] === "undefined") {
+        return;
+      }
+
+      var keys = this._handles[handleId];
+      if (!keys) {
+        keys = [];
+      }
+
+      for (var i = 0; i < keys.length; i++) {
+        this._keys[keys[i]]--;
+      }
+      delete this._handles[handleId];
+
+      this._updateValue();
+    }
+  }, {
+    key: "value",
+    get: function get() {
+      return this._value;
+    }
+  }, {
+    key: "_allKeys",
+    get: function get() {
+      var allKeys = Object.keys(this._keys);
+      allKeys.sort(naturalComparator);
+      return allKeys;
+    }
+  }]);
+
+  return FilterSet;
+}();
+
+exports.default = FilterSet;
+
+},{"./util":11}],4:[function(require,module,exports){
+(function (global){
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+
+var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
+
+var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; };
+
+exports.default = group;
+
+var _var2 = require("./var");
+
+var _var3 = _interopRequireDefault(_var2);
+
+function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
+
+function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
+
+// Use a global so that multiple copies of crosstalk.js can be loaded and still
+// have groups behave as singletons across all copies.
+global.__crosstalk_groups = global.__crosstalk_groups || {};
+var groups = global.__crosstalk_groups;
+
+function group(groupName) {
+  if (groupName && typeof groupName === "string") {
+    if (!groups.hasOwnProperty(groupName)) {
+      groups[groupName] = new Group(groupName);
+    }
+    return groups[groupName];
+  } else if ((typeof groupName === "undefined" ? "undefined" : _typeof(groupName)) === "object" && groupName._vars && groupName.var) {
+    // Appears to already be a group object
+    return groupName;
+  } else if (Array.isArray(groupName) && groupName.length == 1 && typeof groupName[0] === "string") {
+    return group(groupName[0]);
+  } else {
+    throw new Error("Invalid groupName argument");
+  }
+}
+
+var Group = function () {
+  function Group(name) {
+    _classCallCheck(this, Group);
+
+    this.name = name;
+    this._vars = {};
+  }
+
+  _createClass(Group, [{
+    key: "var",
+    value: function _var(name) {
+      if (!name || typeof name !== "string") {
+        throw new Error("Invalid var name");
+      }
+
+      if (!this._vars.hasOwnProperty(name)) this._vars[name] = new _var3.default(this, name);
+      return this._vars[name];
+    }
+  }, {
+    key: "has",
+    value: function has(name) {
+      if (!name || typeof name !== "string") {
+        throw new Error("Invalid var name");
+      }
+
+      return this._vars.hasOwnProperty(name);
+    }
+  }]);
+
+  return Group;
+}();
+
+}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
+
+},{"./var":12}],5:[function(require,module,exports){
+(function (global){
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+
+var _group = require("./group");
+
+var _group2 = _interopRequireDefault(_group);
+
+var _selection = require("./selection");
+
+var _filter = require("./filter");
+
+var _input = require("./input");
+
+require("./input_selectize");
+
+require("./input_checkboxgroup");
+
+require("./input_slider");
+
+function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
+
+var defaultGroup = (0, _group2.default)("default");
+
+function var_(name) {
+  return defaultGroup.var(name);
+}
+
+function has(name) {
+  return defaultGroup.has(name);
+}
+
+if (global.Shiny) {
+  global.Shiny.addCustomMessageHandler("update-client-value", function (message) {
+    if (typeof message.group === "string") {
+      (0, _group2.default)(message.group).var(message.name).set(message.value);
+    } else {
+      var_(message.name).set(message.value);
+    }
+  });
+}
+
+var crosstalk = {
+  group: _group2.default,
+  var: var_,
+  has: has,
+  SelectionHandle: _selection.SelectionHandle,
+  FilterHandle: _filter.FilterHandle,
+  bind: _input.bind
+};
+
+/**
+ * @namespace crosstalk
+ */
+exports.default = crosstalk;
+
+global.crosstalk = crosstalk;
+
+}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
+
+},{"./filter":2,"./group":4,"./input":6,"./input_checkboxgroup":7,"./input_selectize":8,"./input_slider":9,"./selection":10}],6:[function(require,module,exports){
+(function (global){
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.register = register;
+exports.bind = bind;
+var $ = global.jQuery;
+
+var bindings = {};
+
+function register(reg) {
+  bindings[reg.className] = reg;
+  if (global.document && global.document.readyState !== "complete") {
+    $(function () {
+      bind();
+    });
+  } else if (global.document) {
+    setTimeout(bind, 100);
+  }
+}
+
+function bind() {
+  Object.keys(bindings).forEach(function (className) {
+    var binding = bindings[className];
+    $("." + binding.className).not(".crosstalk-input-bound").each(function (i, el) {
+      bindInstance(binding, el);
+    });
+  });
+}
+
+// Escape jQuery identifier
+function $escape(val) {
+  return val.replace(/([!"#$%&'()*+,./:;<=>?@[\\\]^`{|}~])/g, "\\$1");
+}
+
+function bindEl(el) {
+  var $el = $(el);
+  Object.keys(bindings).forEach(function (className) {
+    if ($el.hasClass(className) && !$el.hasClass("crosstalk-input-bound")) {
+      var binding = bindings[className];
+      bindInstance(binding, el);
+    }
+  });
+}
+
+function bindInstance(binding, el) {
+  var jsonEl = $(el).find("script[type='application/json'][data-for='" + $escape(el.id) + "']");
+  var data = JSON.parse(jsonEl[0].innerText);
+
+  var instance = binding.factory(el, data);
+  $(el).data("crosstalk-instance", instance);
+  $(el).addClass("crosstalk-input-bound");
+}
+
+if (global.Shiny) {
+  var inputBinding = new global.Shiny.InputBinding();
+  var _$ = global.jQuery;
+  _$.extend(inputBinding, {
+    find: function find(scope) {
+      return _$(scope).find(".crosstalk-input");
+    },
+    initialize: function initialize(el) {
+      if (!_$(el).hasClass("crosstalk-input-bound")) {
+        bindEl(el);
+      }
+    },
+    getId: function getId(el) {
+      return el.id;
+    },
+    getValue: function getValue(el) {},
+    setValue: function setValue(el, value) {},
+    receiveMessage: function receiveMessage(el, data) {},
+    subscribe: function subscribe(el, callback) {
+      _$(el).data("crosstalk-instance").resume();
+    },
+    unsubscribe: function unsubscribe(el) {
+      _$(el).data("crosstalk-instance").suspend();
+    }
+  });
+  global.Shiny.inputBindings.register(inputBinding, "crosstalk.inputBinding");
+}
+
+}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
+
+},{}],7:[function(require,module,exports){
+(function (global){
+"use strict";
+
+var _input = require("./input");
+
+var input = _interopRequireWildcard(_input);
+
+var _filter = require("./filter");
+
+function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } }
+
+var $ = global.jQuery;
+
+input.register({
+  className: "crosstalk-input-checkboxgroup",
+
+  factory: function factory(el, data) {
+    /*
+     * map: {"groupA": ["keyA", "keyB", ...], ...}
+     * group: "ct-groupname"
+     */
+    var ctHandle = new _filter.FilterHandle(data.group);
+
+    var lastKnownKeys = void 0;
+    var $el = $(el);
+    $el.on("change", "input[type='checkbox']", function () {
+      var checked = $el.find("input[type='checkbox']:checked");
+      if (checked.length === 0) {
+        lastKnownKeys = null;
+        ctHandle.clear();
+      } else {
+        var keys = {};
+        checked.each(function () {
+          data.map[this.value].forEach(function (key) {
+            keys[key] = true;
+          });
+        });
+        var keyArray = Object.keys(keys);
+        keyArray.sort();
+        lastKnownKeys = keyArray;
+        ctHandle.set(keyArray);
+      }
+    });
+
+    return {
+      suspend: function suspend() {
+        ctHandle.clear();
+      },
+      resume: function resume() {
+        if (lastKnownKeys) ctHandle.set(lastKnownKeys);
+      }
+    };
+  }
+});
+
+}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
+
+},{"./filter":2,"./input":6}],8:[function(require,module,exports){
+(function (global){
+"use strict";
+
+var _input = require("./input");
+
+var input = _interopRequireWildcard(_input);
+
+var _util = require("./util");
+
+var util = _interopRequireWildcard(_util);
+
+var _filter = require("./filter");
+
+function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } }
+
+var $ = global.jQuery;
+
+input.register({
+  className: "crosstalk-input-select",
+
+  factory: function factory(el, data) {
+    /*
+     * items: {value: [...], label: [...]}
+     * map: {"groupA": ["keyA", "keyB", ...], ...}
+     * group: "ct-groupname"
+     */
+
+    var first = [{ value: "", label: "(All)" }];
+    var items = util.dataframeToD3(data.items);
+    var opts = {
+      options: first.concat(items),
+      valueField: "value",
+      labelField: "label",
+      searchField: "label"
+    };
+
+    var select = $(el).find("select")[0];
+
+    var selectize = $(select).selectize(opts)[0].selectize;
+
+    var ctHandle = new _filter.FilterHandle(data.group);
+
+    var lastKnownKeys = void 0;
+    selectize.on("change", function () {
+      if (selectize.items.length === 0) {
+        lastKnownKeys = null;
+        ctHandle.clear();
+      } else {
+        var keys = {};
+        selectize.items.forEach(function (group) {
+          data.map[group].forEach(function (key) {
+            keys[key] = true;
+          });
+        });
+        var keyArray = Object.keys(keys);
+        keyArray.sort();
+        lastKnownKeys = keyArray;
+        ctHandle.set(keyArray);
+      }
+    });
+
+    return {
+      suspend: function suspend() {
+        ctHandle.clear();
+      },
+      resume: function resume() {
+        if (lastKnownKeys) ctHandle.set(lastKnownKeys);
+      }
+    };
+  }
+});
+
+}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
+
+},{"./filter":2,"./input":6,"./util":11}],9:[function(require,module,exports){
+(function (global){
+"use strict";
+
+var _slicedToArray = function () { function sliceIterator(arr, i) { var _arr = []; var _n = true; var _d = false; var _e = undefined; try { for (var _i = arr[Symbol.iterator](), _s; !(_n = (_s = _i.next()).done); _n = true) { _arr.push(_s.value); if (i && _arr.length === i) break; } } catch (err) { _d = true; _e = err; } finally { try { if (!_n && _i["return"]) _i["return"](); } finally { if (_d) throw _e; } } return _arr; } return function (arr, i) { if (Array.isArray(arr)) { return arr; } else if (Symbol.iterator in Object(arr)) { return sliceIterator(arr, i); } else { throw new TypeError("Invalid attempt to destructure non-iterable instance"); } }; }();
+
+var _input = require("./input");
+
+var input = _interopRequireWildcard(_input);
+
+var _filter = require("./filter");
+
+function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } }
+
+var $ = global.jQuery;
+var strftime = global.strftime;
+
+input.register({
+  className: "crosstalk-input-slider",
+
+  factory: function factory(el, data) {
+    /*
+     * map: {"groupA": ["keyA", "keyB", ...], ...}
+     * group: "ct-groupname"
+     */
+    var ctHandle = new _filter.FilterHandle(data.group);
+
+    var opts = {};
+    var $el = $(el).find("input");
+    var dataType = $el.data("data-type");
+    var timeFormat = $el.data("time-format");
+    var round = $el.data("round");
+    var timeFormatter = void 0;
+
+    // Set up formatting functions
+    if (dataType === "date") {
+      timeFormatter = strftime.utc();
+      opts.prettify = function (num) {
+        return timeFormatter(timeFormat, new Date(num));
+      };
+    } else if (dataType === "datetime") {
+      var timezone = $el.data("timezone");
+      if (timezone) timeFormatter = strftime.timezone(timezone);else timeFormatter = strftime;
+
+      opts.prettify = function (num) {
+        return timeFormatter(timeFormat, new Date(num));
+      };
+    } else if (dataType === "number") {
+      if (typeof round !== "undefined") opts.prettify = function (num) {
+        var factor = Math.pow(10, round);
+        return Math.round(num * factor) / factor;
+      };
+    }
+
+    $el.ionRangeSlider(opts);
+
+    function getValue() {
+      var result = $el.data("ionRangeSlider").result;
+
+      // Function for converting numeric value from slider to appropriate type.
+      var convert = void 0;
+      var dataType = $el.data("data-type");
+      if (dataType === "date") {
+        convert = function convert(val) {
+          return formatDateUTC(new Date(+val));
+        };
+      } else if (dataType === "datetime") {
+        convert = function convert(val) {
+          // Convert ms to s
+          return +val / 1000;
+        };
+      } else {
+        convert = function convert(val) {
+          return +val;
+        };
+      }
+
+      if ($el.data("ionRangeSlider").options.type === "double") {
+        return [convert(result.from), convert(result.to)];
+      } else {
+        return convert(result.from);
+      }
+    }
+
+    var lastKnownKeys = null;
+
+    $el.on("change.crosstalkSliderInput", function (event) {
+      if (!$el.data("updating") && !$el.data("animating")) {
+        var _getValue = getValue(),
+            _getValue2 = _slicedToArray(_getValue, 2),
+            from = _getValue2[0],
+            to = _getValue2[1];
+
+        var keys = [];
+        for (var i = 0; i < data.values.length; i++) {
+          var val = data.values[i];
+          if (val >= from && val <= to) {
+            keys.push(data.keys[i]);
+          }
+        }
+        keys.sort();
+        ctHandle.set(keys);
+        lastKnownKeys = keys;
+      }
+    });
+
+    // let $el = $(el);
+    // $el.on("change", "input[type="checkbox"]", function() {
+    //   let checked = $el.find("input[type="checkbox"]:checked");
+    //   if (checked.length === 0) {
+    //     ctHandle.clear();
+    //   } else {
+    //     let keys = {};
+    //     checked.each(function() {
+    //       data.map[this.value].forEach(function(key) {
+    //         keys[key] = true;
+    //       });
+    //     });
+    //     let keyArray = Object.keys(keys);
+    //     keyArray.sort();
+    //     ctHandle.set(keyArray);
+    //   }
+    // });
+
+    return {
+      suspend: function suspend() {
+        ctHandle.clear();
+      },
+      resume: function resume() {
+        if (lastKnownKeys) ctHandle.set(lastKnownKeys);
+      }
+    };
+  }
+});
+
+// Convert a number to a string with leading zeros
+function padZeros(n, digits) {
+  var str = n.toString();
+  while (str.length < digits) {
+    str = "0" + str;
+  }return str;
+}
+
+// Given a Date object, return a string in yyyy-mm-dd format, using the
+// UTC date. This may be a day off from the date in the local time zone.
+function formatDateUTC(date) {
+  if (date instanceof Date) {
+    return date.getUTCFullYear() + "-" + padZeros(date.getUTCMonth() + 1, 2) + "-" + padZeros(date.getUTCDate(), 2);
+  } else {
+    return null;
+  }
+}
+
+}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
+
+},{"./filter":2,"./input":6}],10:[function(require,module,exports){
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.SelectionHandle = undefined;
+
+var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
+
+var _events = require("./events");
+
+var _events2 = _interopRequireDefault(_events);
+
+var _group = require("./group");
+
+var _group2 = _interopRequireDefault(_group);
+
+var _util = require("./util");
+
+var util = _interopRequireWildcard(_util);
+
+function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } }
+
+function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
+
+function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
+
+/**
+ * Use this class to read and write (and listen for changes to) the selection
+ * for a Crosstalk group. This is intended to be used for linked brushing.
+ *
+ * If two (or more) `SelectionHandle` instances in the same webpage share the
+ * same group name, they will share the same state. Setting the selection using
+ * one `SelectionHandle` instance will result in the `value` property instantly
+ * changing across the others, and `"change"` event listeners on all instances
+ * (including the one that initiated the sending) will fire.
+ *
+ * @param {string} [group] - The name of the Crosstalk group, or if none,
+ *   null or undefined (or any other falsy value). This can be changed later
+ *   via the [SelectionHandle#setGroup](#setGroup) method.
+ * @param {Object} [extraInfo] - An object whose properties will be copied to
+ *   the event object whenever an event is emitted.
+ */
+var SelectionHandle = exports.SelectionHandle = function () {
+  function SelectionHandle() {
+    var group = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null;
+    var extraInfo = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null;
+
+    _classCallCheck(this, SelectionHandle);
+
+    this._eventRelay = new _events2.default();
+    this._emitter = new util.SubscriptionTracker(this._eventRelay);
+
+    // Name of the group we're currently tracking, if any. Can change over time.
+    this._group = null;
+    // The Var we're currently tracking, if any. Can change over time.
+    this._var = null;
+    // The event handler subscription we currently have on var.on("change").
+    this._varOnChangeSub = null;
+
+    this._extraInfo = util.extend({ sender: this }, extraInfo);
+
+    this.setGroup(group);
+  }
+
+  /**
+   * Changes the Crosstalk group membership of this SelectionHandle. The group
+   * being switched away from (if any) will not have its selection value
+   * modified as a result of calling `setGroup`, even if this handle was the
+   * most recent handle to set the selection of the group.
+   *
+   * The group being switched to (if any) will also not have its selection value
+   * modified as a result of calling `setGroup`. If you want to set the
+   * selection value of the new group, call `set` explicitly.
+   *
+   * @param {string} group - The name of the Crosstalk group, or null (or
+   *   undefined) to clear the group.
+   */
+
+
+  _createClass(SelectionHandle, [{
+    key: "setGroup",
+    value: function setGroup(group) {
+      var _this = this;
+
+      // If group is unchanged, do nothing
+      if (this._group === group) return;
+      // Treat null, undefined, and other falsy values the same
+      if (!this._group && !group) return;
+
+      if (this._var) {
+        this._var.off("change", this._varOnChangeSub);
+        this._var = null;
+        this._varOnChangeSub = null;
+      }
+
+      this._group = group;
+
+      if (group) {
+        this._var = (0, _group2.default)(group).var("selection");
+        var sub = this._var.on("change", function (e) {
+          _this._eventRelay.trigger("change", e, _this);
+        });
+        this._varOnChangeSub = sub;
+      }
+    }
+
+    /**
+     * Retrieves the current selection for the group represented by this
+     * `SelectionHandle`.
+     *
+     * - If no selection is active, then this value will be falsy.
+     * - If a selection is active, but no data points are selected, then this
+     *   value will be an empty array.
+     * - If a selection is active, and data points are selected, then the keys
+     *   of the selected data points will be present in the array.
+     */
+
+  }, {
+    key: "_mergeExtraInfo",
+
+
+    /**
+     * Combines the given `extraInfo` (if any) with the handle's default
+     * `_extraInfo` (if any).
+     * @private
+     */
+    value: function _mergeExtraInfo(extraInfo) {
+      // Important incidental effect: shallow clone is returned
+      return util.extend({}, this._extraInfo ? this._extraInfo : null, extraInfo ? extraInfo : null);
+    }
+
+    /**
+     * Overwrites the current selection for the group, and raises the `"change"`
+     * event among all of the group's '`SelectionHandle` instances (including
+     * this one).
+     *
+     * @fires SelectionHandle#change
+     * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see
+     *   {@link SelectionHandle#value}).
+     * @param {Object} [extraInfo] - Extra properties to be included on the event
+     *   object that's passed to listeners (in addition to any options that were
+     *   passed into the `SelectionHandle` constructor).
+     */
+
+  }, {
+    key: "set",
+    value: function set(selectedKeys, extraInfo) {
+      if (this._var) this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));
+    }
+
+    /**
+     * Overwrites the current selection for the group, and raises the `"change"`
+     * event among all of the group's '`SelectionHandle` instances (including
+     * this one).
+     *
+     * @fires SelectionHandle#change
+     * @param {Object} [extraInfo] - Extra properties to be included on the event
+     *   object that's passed to listeners (in addition to any that were passed
+     *   into the `SelectionHandle` constructor).
+     */
+
+  }, {
+    key: "clear",
+    value: function clear(extraInfo) {
+      if (this._var) this.set(void 0, this._mergeExtraInfo(extraInfo));
+    }
+
+    /**
+     * Subscribes to events on this `SelectionHandle`.
+     *
+     * @param {string} eventType - Indicates the type of events to listen to.
+     *   Currently, only `"change"` is supported.
+     * @param {SelectionHandle~listener} listener - The callback function that
+     *   will be invoked when the event occurs.
+     * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel
+     *   this subscription.
+     */
+
+  }, {
+    key: "on",
+    value: function on(eventType, listener) {
+      return this._emitter.on(eventType, listener);
+    }
+
+    /**
+     * Cancels event subscriptions created by {@link SelectionHandle#on}.
+     *
+     * @param {string} eventType - The type of event to unsubscribe.
+     * @param {string|SelectionHandle~listener} listener - Either the callback
+     *   function previously passed into {@link SelectionHandle#on}, or the
+     *   string that was returned from {@link SelectionHandle#on}.
+     */
+
+  }, {
+    key: "off",
+    value: function off(eventType, listener) {
+      return this._emitter.off(eventType, listener);
+    }
+
+    /**
+     * Shuts down the `SelectionHandle` object.
+     *
+     * Removes all event listeners that were added through this handle.
+     */
+
+  }, {
+    key: "close",
+    value: function close() {
+      this._emitter.removeAllListeners();
+      this.setGroup(null);
+    }
+  }, {
+    key: "value",
+    get: function get() {
+      return this._var ? this._var.get() : null;
+    }
+  }]);
+
+  return SelectionHandle;
+}();
+
+/**
+ * @callback SelectionHandle~listener
+ * @param {Object} event - An object containing details of the event. For
+ *   `"change"` events, this includes the properties `value` (the new
+ *   value of the selection, or `undefined` if no selection is active),
+ *   `oldValue` (the previous value of the selection), and `sender` (the
+ *   `SelectionHandle` instance that made the change).
+ */
+
+/**
+ * @event SelectionHandle#change
+ * @type {object}
+ * @property {object} value - The new value of the selection, or `undefined`
+ *   if no selection is active.
+ * @property {object} oldValue - The previous value of the selection.
+ * @property {SelectionHandle} sender - The `SelectionHandle` instance that
+ *   changed the value.
+ */
+
+},{"./events":1,"./group":4,"./util":11}],11:[function(require,module,exports){
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+
+var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
+
+var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; };
+
+exports.extend = extend;
+exports.checkSorted = checkSorted;
+exports.diffSortedLists = diffSortedLists;
+exports.dataframeToD3 = dataframeToD3;
+
+function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
+
+function extend(target) {
+  for (var _len = arguments.length, sources = Array(_len > 1 ? _len - 1 : 0), _key = 1; _key < _len; _key++) {
+    sources[_key - 1] = arguments[_key];
+  }
+
+  for (var i = 0; i < sources.length; i++) {
+    var src = sources[i];
+    if (typeof src === "undefined" || src === null) continue;
+
+    for (var key in src) {
+      if (src.hasOwnProperty(key)) {
+        target[key] = src[key];
+      }
+    }
+  }
+  return target;
+}
+
+function checkSorted(list) {
+  for (var i = 1; i < list.length; i++) {
+    if (list[i] <= list[i - 1]) {
+      throw new Error("List is not sorted or contains duplicate");
+    }
+  }
+}
+
+function diffSortedLists(a, b) {
+  var i_a = 0;
+  var i_b = 0;
+
+  if (!a) a = [];
+  if (!b) b = [];
+
+  var a_only = [];
+  var b_only = [];
+
+  checkSorted(a);
+  checkSorted(b);
+
+  while (i_a < a.length && i_b < b.length) {
+    if (a[i_a] === b[i_b]) {
+      i_a++;
+      i_b++;
+    } else if (a[i_a] < b[i_b]) {
+      a_only.push(a[i_a++]);
+    } else {
+      b_only.push(b[i_b++]);
+    }
+  }
+
+  if (i_a < a.length) a_only = a_only.concat(a.slice(i_a));
+  if (i_b < b.length) b_only = b_only.concat(b.slice(i_b));
+  return {
+    removed: a_only,
+    added: b_only
+  };
+}
+
+// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }
+// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]
+function dataframeToD3(df) {
+  var names = [];
+  var length = void 0;
+  for (var name in df) {
+    if (df.hasOwnProperty(name)) names.push(name);
+    if (_typeof(df[name]) !== "object" || typeof df[name].length === "undefined") {
+      throw new Error("All fields must be arrays");
+    } else if (typeof length !== "undefined" && length !== df[name].length) {
+      throw new Error("All fields must be arrays of the same length");
+    }
+    length = df[name].length;
+  }
+  var results = [];
+  var item = void 0;
+  for (var row = 0; row < length; row++) {
+    item = {};
+    for (var col = 0; col < names.length; col++) {
+      item[names[col]] = df[names[col]][row];
+    }
+    results.push(item);
+  }
+  return results;
+}
+
+/**
+ * Keeps track of all event listener additions/removals and lets all active
+ * listeners be removed with a single operation.
+ *
+ * @private
+ */
+
+var SubscriptionTracker = exports.SubscriptionTracker = function () {
+  function SubscriptionTracker(emitter) {
+    _classCallCheck(this, SubscriptionTracker);
+
+    this._emitter = emitter;
+    this._subs = {};
+  }
+
+  _createClass(SubscriptionTracker, [{
+    key: "on",
+    value: function on(eventType, listener) {
+      var sub = this._emitter.on(eventType, listener);
+      this._subs[sub] = eventType;
+      return sub;
+    }
+  }, {
+    key: "off",
+    value: function off(eventType, listener) {
+      var sub = this._emitter.off(eventType, listener);
+      if (sub) {
+        delete this._subs[sub];
+      }
+      return sub;
+    }
+  }, {
+    key: "removeAllListeners",
+    value: function removeAllListeners() {
+      var _this = this;
+
+      var current_subs = this._subs;
+      this._subs = {};
+      Object.keys(current_subs).forEach(function (sub) {
+        _this._emitter.off(current_subs[sub], sub);
+      });
+    }
+  }]);
+
+  return SubscriptionTracker;
+}();
+
+},{}],12:[function(require,module,exports){
+(function (global){
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+
+var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; };
+
+var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
+
+var _events = require("./events");
+
+var _events2 = _interopRequireDefault(_events);
+
+function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
+
+function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
+
+var Var = function () {
+  function Var(group, name, /*optional*/value) {
+    _classCallCheck(this, Var);
+
+    this._group = group;
+    this._name = name;
+    this._value = value;
+    this._events = new _events2.default();
+  }
+
+  _createClass(Var, [{
+    key: "get",
+    value: function get() {
+      return this._value;
+    }
+  }, {
+    key: "set",
+    value: function set(value, /*optional*/event) {
+      if (this._value === value) {
+        // Do nothing; the value hasn't changed
+        return;
+      }
+      var oldValue = this._value;
+      this._value = value;
+      // Alert JavaScript listeners that the value has changed
+      var evt = {};
+      if (event && (typeof event === "undefined" ? "undefined" : _typeof(event)) === "object") {
+        for (var k in event) {
+          if (event.hasOwnProperty(k)) evt[k] = event[k];
+        }
+      }
+      evt.oldValue = oldValue;
+      evt.value = value;
+      this._events.trigger("change", evt, this);
+
+      // TODO: Make this extensible, to let arbitrary back-ends know that
+      // something has changed
+      if (global.Shiny && global.Shiny.onInputChange) {
+        global.Shiny.onInputChange(".clientValue-" + (this._group.name !== null ? this._group.name + "-" : "") + this._name, typeof value === "undefined" ? null : value);
+      }
+    }
+  }, {
+    key: "on",
+    value: function on(eventType, listener) {
+      return this._events.on(eventType, listener);
+    }
+  }, {
+    key: "off",
+    value: function off(eventType, listener) {
+      return this._events.off(eventType, listener);
+    }
+  }]);
+
+  return Var;
+}();
+
+exports.default = Var;
+
+}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
+
+},{"./events":1}]},{},[5])
+//# sourceMappingURL=crosstalk.js.map
diff --git a/docs/articles/scFlow_files/crosstalk-1.2.1/js/crosstalk.js.map b/docs/articles/scFlow_files/crosstalk-1.2.1/js/crosstalk.js.map
new file mode 100644
index 0000000..cff94f0
--- /dev/null
+++ b/docs/articles/scFlow_files/crosstalk-1.2.1/js/crosstalk.js.map
@@ -0,0 +1,37 @@
+{
+  "version": 3,
+  "sources": [
+    "node_modules/browser-pack/_prelude.js",
+    "javascript/src/events.js",
+    "javascript/src/filter.js",
+    "javascript/src/filterset.js",
+    "javascript/src/group.js",
+    "javascript/src/index.js",
+    "javascript/src/input.js",
+    "javascript/src/input_checkboxgroup.js",
+    "javascript/src/input_selectize.js",
+    "javascript/src/input_slider.js",
+    "javascript/src/selection.js",
+    "javascript/src/util.js",
+    "javascript/src/var.js"
+  ],
+  "names": [],
+  "mappings": 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+  "sourceRoot": "",
+  "sourcesContent": [
+    "(function(){function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require==\"function\"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error(\"Cannot find module '\"+o+\"'\");throw f.code=\"MODULE_NOT_FOUND\",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require==\"function\"&&require;for(var o=0;o {\n        this._eventRelay.trigger(\"change\", e, this);\n      });\n      this._varOnChangeSub = sub;\n    }\n  }\n\n  /**\n   * Combine the given `extraInfo` (if any) with the handle's default\n   * `_extraInfo` (if any).\n   * @private\n   */\n  _mergeExtraInfo(extraInfo) {\n    return util.extend({},\n      this._extraInfo ? this._extraInfo : null,\n      extraInfo ? extraInfo : null);\n  }\n\n  /**\n   * Close the handle. This clears this handle's contribution to the filter set,\n   * and unsubscribes all event listeners.\n   */\n  close() {\n    this._emitter.removeAllListeners();\n    this.clear();\n    this.setGroup(null);\n  }\n\n  /**\n   * Clear this handle's contribution to the filter set.\n   *\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any options that were\n   *   passed into the `FilterHandle` constructor).\n   * \n   * @fires FilterHandle#change\n   */\n  clear(extraInfo) {\n    if (!this._filterSet)\n      return;\n    this._filterSet.clear(this._id);\n    this._onChange(extraInfo);\n  }\n\n  /**\n   * Set this handle's contribution to the filter set. This array should consist\n   * of the keys of the rows that _should_ be displayed; any keys that are not\n   * present in the array will be considered _filtered out_. Note that multiple\n   * `FilterHandle` instances in the group may each contribute an array of keys,\n   * and only those keys that appear in _all_ of the arrays make it through the\n   * filter.\n   *\n   * @param {string[]} keys - Empty array, or array of keys. To clear the\n   *   filter, don't pass an empty array; instead, use the\n   *   {@link FilterHandle#clear} method.\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any options that were\n   *   passed into the `FilterHandle` constructor).\n   * \n   * @fires FilterHandle#change\n   */\n  set(keys, extraInfo) {\n    if (!this._filterSet)\n      return;\n    this._filterSet.update(this._id, keys);\n    this._onChange(extraInfo);\n  }\n\n  /**\n   * @return {string[]|null} - Either: 1) an array of keys that made it through\n   *   all of the `FilterHandle` instances, or, 2) `null`, which means no filter\n   *   is being applied (all data should be displayed).\n   */\n  get filteredKeys() {\n    return this._filterSet ? this._filterSet.value : null;\n  }\n\n  /**\n   * Subscribe to events on this `FilterHandle`.\n   *\n   * @param {string} eventType - Indicates the type of events to listen to.\n   *   Currently, only `\"change\"` is supported.\n   * @param {FilterHandle~listener} listener - The callback function that\n   *   will be invoked when the event occurs.\n   * @return {string} - A token to pass to {@link FilterHandle#off} to cancel\n   *   this subscription.\n   */\n  on(eventType, listener) {\n    return this._emitter.on(eventType, listener);\n  }\n\n  /**\n   * Cancel event subscriptions created by {@link FilterHandle#on}.\n   *\n   * @param {string} eventType - The type of event to unsubscribe.\n   * @param {string|FilterHandle~listener} listener - Either the callback\n   *   function previously passed into {@link FilterHandle#on}, or the\n   *   string that was returned from {@link FilterHandle#on}.\n   */\n  off(eventType, listener) {\n    return this._emitter.off(eventType, listener);\n  }\n\n  _onChange(extraInfo) {\n    if (!this._filterSet)\n      return;\n    this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));\n  }\n\n  /**\n   * @callback FilterHandle~listener\n   * @param {Object} event - An object containing details of the event. For\n   *   `\"change\"` events, this includes the properties `value` (the new\n   *   value of the filter set, or `null` if no filter set is active),\n   *   `oldValue` (the previous value of the filter set), and `sender` (the\n   *   `FilterHandle` instance that made the change).\n   */\n\n}\n\n/**\n * @event FilterHandle#change\n * @type {object}\n * @property {object} value - The new value of the filter set, or `null`\n *   if no filter set is active.\n * @property {object} oldValue - The previous value of the filter set.\n * @property {FilterHandle} sender - The `FilterHandle` instance that\n *   changed the value.\n */\n",
+    "import { diffSortedLists } from \"./util\";\n\nfunction naturalComparator(a, b) {\n  if (a === b) {\n    return 0;\n  } else if (a < b) {\n    return -1;\n  } else if (a > b) {\n    return 1;\n  }\n}\n\n/**\n * @private\n */\nexport default class FilterSet {\n  constructor() {\n    this.reset();\n  }\n\n  reset() {\n    // Key: handle ID, Value: array of selected keys, or null\n    this._handles = {};\n    // Key: key string, Value: count of handles that include it\n    this._keys = {};\n    this._value = null;\n    this._activeHandles = 0;\n  }\n\n  get value() {\n    return this._value;\n  }\n\n  update(handleId, keys) {\n    if (keys !== null) {\n      keys = keys.slice(0); // clone before sorting\n      keys.sort(naturalComparator);\n    }\n\n    let {added, removed} = diffSortedLists(this._handles[handleId], keys);\n    this._handles[handleId] = keys;\n\n    for (let i = 0; i < added.length; i++) {\n      this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;\n    }\n    for (let i = 0; i < removed.length; i++) {\n      this._keys[removed[i]]--;\n    }\n\n    this._updateValue(keys);\n  }\n\n  /**\n   * @param {string[]} keys Sorted array of strings that indicate\n   * a superset of possible keys.\n   * @private\n   */\n  _updateValue(keys = this._allKeys) {\n    let handleCount = Object.keys(this._handles).length;\n    if (handleCount === 0) {\n      this._value = null;\n    } else {\n      this._value = [];\n      for (let i = 0; i < keys.length; i++) {\n        let count = this._keys[keys[i]];\n        if (count === handleCount) {\n          this._value.push(keys[i]);\n        }\n      }\n    }\n  }\n\n  clear(handleId) {\n    if (typeof(this._handles[handleId]) === \"undefined\") {\n      return;\n    }\n\n    let keys = this._handles[handleId];\n    if (!keys) {\n      keys = [];\n    }\n\n    for (let i = 0; i < keys.length; i++) {\n      this._keys[keys[i]]--;\n    }\n    delete this._handles[handleId];\n\n    this._updateValue();\n  }\n\n  get _allKeys() {\n    let allKeys = Object.keys(this._keys);\n    allKeys.sort(naturalComparator);\n    return allKeys;\n  }\n}\n",
+    "import Var from \"./var\";\n\n// Use a global so that multiple copies of crosstalk.js can be loaded and still\n// have groups behave as singletons across all copies.\nglobal.__crosstalk_groups = global.__crosstalk_groups || {};\nlet groups = global.__crosstalk_groups;\n\nexport default function group(groupName) {\n  if (groupName && typeof(groupName) === \"string\") {\n    if (!groups.hasOwnProperty(groupName)) {\n      groups[groupName] = new Group(groupName);\n    }\n    return groups[groupName];\n  } else if (typeof(groupName) === \"object\" && groupName._vars && groupName.var) {\n    // Appears to already be a group object\n    return groupName;\n  } else if (Array.isArray(groupName) &&\n      groupName.length == 1 &&\n      typeof(groupName[0]) === \"string\") {\n    return group(groupName[0]);\n  } else {\n    throw new Error(\"Invalid groupName argument\");\n  }\n}\n\nclass Group {\n  constructor(name) {\n    this.name = name;\n    this._vars = {};\n  }\n\n  var(name) {\n    if (!name || typeof(name) !== \"string\") {\n      throw new Error(\"Invalid var name\");\n    }\n\n    if (!this._vars.hasOwnProperty(name))\n      this._vars[name] = new Var(this, name);\n    return this._vars[name];\n  }\n\n  has(name) {\n    if (!name || typeof(name) !== \"string\") {\n      throw new Error(\"Invalid var name\");\n    }\n\n    return this._vars.hasOwnProperty(name);\n  }\n}\n",
+    "import group from \"./group\";\nimport { SelectionHandle } from \"./selection\";\nimport { FilterHandle } from \"./filter\";\nimport { bind } from \"./input\";\nimport \"./input_selectize\";\nimport \"./input_checkboxgroup\";\nimport \"./input_slider\";\n\nconst defaultGroup = group(\"default\");\n\nfunction var_(name) {\n  return defaultGroup.var(name);\n}\n\nfunction has(name) {\n  return defaultGroup.has(name);\n}\n\nif (global.Shiny) {\n  global.Shiny.addCustomMessageHandler(\"update-client-value\", function(message) {\n    if (typeof(message.group) === \"string\") {\n      group(message.group).var(message.name).set(message.value);\n    } else {\n      var_(message.name).set(message.value);\n    }\n  });\n}\n\nconst crosstalk = {\n  group: group,\n  var: var_,\n  has: has,\n  SelectionHandle: SelectionHandle,\n  FilterHandle: FilterHandle,\n  bind: bind\n};\n\n/**\n * @namespace crosstalk\n */\nexport default crosstalk;\nglobal.crosstalk = crosstalk;\n",
+    "let $ = global.jQuery;\n\nlet bindings = {};\n\nexport function register(reg) {\n  bindings[reg.className] = reg;\n  if (global.document && global.document.readyState !== \"complete\") {\n    $(() => {\n      bind();\n    });\n  } else if (global.document) {\n    setTimeout(bind, 100);\n  }\n}\n\nexport function bind() {\n  Object.keys(bindings).forEach(function(className) {\n    let binding = bindings[className];\n    $(\".\" + binding.className).not(\".crosstalk-input-bound\").each(function(i, el) {\n      bindInstance(binding, el);\n    });\n  });\n}\n\n// Escape jQuery identifier\nfunction $escape(val) {\n  return val.replace(/([!\"#$%&'()*+,./:;<=>?@[\\\\\\]^`{|}~])/g, \"\\\\$1\");\n}\n\nfunction bindEl(el) {\n  let $el = $(el);\n  Object.keys(bindings).forEach(function(className) {\n    if ($el.hasClass(className) && !$el.hasClass(\"crosstalk-input-bound\")) {\n      let binding = bindings[className];\n      bindInstance(binding, el);\n    }\n  });\n}\n\nfunction bindInstance(binding, el) {\n  let jsonEl = $(el).find(\"script[type='application/json'][data-for='\" + $escape(el.id) + \"']\");\n  let data = JSON.parse(jsonEl[0].innerText);\n\n  let instance = binding.factory(el, data);\n  $(el).data(\"crosstalk-instance\", instance);\n  $(el).addClass(\"crosstalk-input-bound\");\n}\n\nif (global.Shiny) {\n  let inputBinding = new global.Shiny.InputBinding();\n  let $ = global.jQuery;\n  $.extend(inputBinding, {\n    find: function(scope) {\n      return $(scope).find(\".crosstalk-input\");\n    },\n    initialize: function(el) {\n      if (!$(el).hasClass(\"crosstalk-input-bound\")) {\n        bindEl(el);\n      }\n    },\n    getId: function(el) {\n      return el.id;\n    },\n    getValue: function(el) {\n\n    },\n    setValue: function(el, value) {\n\n    },\n    receiveMessage: function(el, data) {\n\n    },\n    subscribe: function(el, callback) {\n      $(el).data(\"crosstalk-instance\").resume();\n    },\n    unsubscribe: function(el) {\n      $(el).data(\"crosstalk-instance\").suspend();\n    }\n  });\n  global.Shiny.inputBindings.register(inputBinding, \"crosstalk.inputBinding\");\n}\n",
+    "import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n  className: \"crosstalk-input-checkboxgroup\",\n\n  factory: function(el, data) {\n    /*\n     * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n     * group: \"ct-groupname\"\n     */\n    let ctHandle = new FilterHandle(data.group);\n\n    let lastKnownKeys;\n    let $el = $(el);\n    $el.on(\"change\", \"input[type='checkbox']\", function() {\n      let checked = $el.find(\"input[type='checkbox']:checked\");\n      if (checked.length === 0) {\n        lastKnownKeys = null;\n        ctHandle.clear();\n      } else {\n        let keys = {};\n        checked.each(function() {\n          data.map[this.value].forEach(function(key) {\n            keys[key] = true;\n          });\n        });\n        let keyArray = Object.keys(keys);\n        keyArray.sort();\n        lastKnownKeys = keyArray;\n        ctHandle.set(keyArray);\n      }\n    });\n\n    return {\n      suspend: function() {\n        ctHandle.clear();\n      },\n      resume: function() {\n        if (lastKnownKeys)\n          ctHandle.set(lastKnownKeys);\n      }\n    };\n  }\n});\n",
+    "import * as input from \"./input\";\nimport * as util from \"./util\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n  className: \"crosstalk-input-select\",\n\n  factory: function(el, data) {\n    /*\n     * items: {value: [...], label: [...]}\n     * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n     * group: \"ct-groupname\"\n     */\n\n    let first = [{value: \"\", label: \"(All)\"}];\n    let items = util.dataframeToD3(data.items);\n    let opts = {\n      options: first.concat(items),\n      valueField: \"value\",\n      labelField: \"label\",\n      searchField: \"label\"\n    };\n\n    let select = $(el).find(\"select\")[0];\n\n    let selectize = $(select).selectize(opts)[0].selectize;\n\n    let ctHandle = new FilterHandle(data.group);\n\n    let lastKnownKeys;\n    selectize.on(\"change\", function() {\n      if (selectize.items.length === 0) {\n        lastKnownKeys = null;\n        ctHandle.clear();\n      } else {\n        let keys = {};\n        selectize.items.forEach(function(group) {\n          data.map[group].forEach(function(key) {\n            keys[key] = true;\n          });\n        });\n        let keyArray = Object.keys(keys);\n        keyArray.sort();\n        lastKnownKeys = keyArray;\n        ctHandle.set(keyArray);\n      }\n    });\n\n    return {\n      suspend: function() {\n        ctHandle.clear();\n      },\n      resume: function() {\n        if (lastKnownKeys)\n          ctHandle.set(lastKnownKeys);\n      }\n    };\n  }\n});\n",
+    "import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\nlet strftime = global.strftime;\n\ninput.register({\n  className: \"crosstalk-input-slider\",\n\n  factory: function(el, data) {\n    /*\n     * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n     * group: \"ct-groupname\"\n     */\n    let ctHandle = new FilterHandle(data.group);\n\n    let opts = {};\n    let $el = $(el).find(\"input\");\n    let dataType = $el.data(\"data-type\");\n    let timeFormat = $el.data(\"time-format\");\n    let round = $el.data(\"round\");\n    let timeFormatter;\n\n    // Set up formatting functions\n    if (dataType === \"date\") {\n      timeFormatter = strftime.utc();\n      opts.prettify = function(num) {\n        return timeFormatter(timeFormat, new Date(num));\n      };\n\n    } else if (dataType === \"datetime\") {\n      let timezone = $el.data(\"timezone\");\n      if (timezone)\n        timeFormatter = strftime.timezone(timezone);\n      else\n        timeFormatter = strftime;\n\n      opts.prettify = function(num) {\n        return timeFormatter(timeFormat, new Date(num));\n      };\n    } else if (dataType === \"number\") {\n      if (typeof round !== \"undefined\")\n        opts.prettify = function(num) {\n          let factor = Math.pow(10, round);\n          return Math.round(num * factor) / factor;\n        };\n    }\n\n    $el.ionRangeSlider(opts);\n\n    function getValue() {\n      let result = $el.data(\"ionRangeSlider\").result;\n\n      // Function for converting numeric value from slider to appropriate type.\n      let convert;\n      let dataType = $el.data(\"data-type\");\n      if (dataType === \"date\") {\n        convert = function(val) {\n          return formatDateUTC(new Date(+val));\n        };\n      } else if (dataType === \"datetime\") {\n        convert = function(val) {\n          // Convert ms to s\n          return +val / 1000;\n        };\n      } else {\n        convert = function(val) { return +val; };\n      }\n\n      if ($el.data(\"ionRangeSlider\").options.type === \"double\") {\n        return [convert(result.from), convert(result.to)];\n      } else {\n        return convert(result.from);\n      }\n    }\n\n    let lastKnownKeys = null;\n\n    $el.on(\"change.crosstalkSliderInput\", function(event) {\n      if (!$el.data(\"updating\") && !$el.data(\"animating\")) {\n        let [from, to] = getValue();\n        let keys = [];\n        for (let i = 0; i < data.values.length; i++) {\n          let val = data.values[i];\n          if (val >= from && val <= to) {\n            keys.push(data.keys[i]);\n          }\n        }\n        keys.sort();\n        ctHandle.set(keys);\n        lastKnownKeys = keys;\n      }\n    });\n\n\n    // let $el = $(el);\n    // $el.on(\"change\", \"input[type=\"checkbox\"]\", function() {\n    //   let checked = $el.find(\"input[type=\"checkbox\"]:checked\");\n    //   if (checked.length === 0) {\n    //     ctHandle.clear();\n    //   } else {\n    //     let keys = {};\n    //     checked.each(function() {\n    //       data.map[this.value].forEach(function(key) {\n    //         keys[key] = true;\n    //       });\n    //     });\n    //     let keyArray = Object.keys(keys);\n    //     keyArray.sort();\n    //     ctHandle.set(keyArray);\n    //   }\n    // });\n\n    return {\n      suspend: function() {\n        ctHandle.clear();\n      },\n      resume: function() {\n        if (lastKnownKeys)\n          ctHandle.set(lastKnownKeys);\n      }\n    };\n  }\n});\n\n\n// Convert a number to a string with leading zeros\nfunction padZeros(n, digits) {\n  let str = n.toString();\n  while (str.length < digits)\n    str = \"0\" + str;\n  return str;\n}\n\n// Given a Date object, return a string in yyyy-mm-dd format, using the\n// UTC date. This may be a day off from the date in the local time zone.\nfunction formatDateUTC(date) {\n  if (date instanceof Date) {\n    return date.getUTCFullYear() + \"-\" +\n           padZeros(date.getUTCMonth()+1, 2) + \"-\" +\n           padZeros(date.getUTCDate(), 2);\n\n  } else {\n    return null;\n  }\n}\n",
+    "import Events from \"./events\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\n/**\n * Use this class to read and write (and listen for changes to) the selection\n * for a Crosstalk group. This is intended to be used for linked brushing.\n *\n * If two (or more) `SelectionHandle` instances in the same webpage share the\n * same group name, they will share the same state. Setting the selection using\n * one `SelectionHandle` instance will result in the `value` property instantly\n * changing across the others, and `\"change\"` event listeners on all instances\n * (including the one that initiated the sending) will fire.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n *   null or undefined (or any other falsy value). This can be changed later\n *   via the [SelectionHandle#setGroup](#setGroup) method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n *   the event object whenever an event is emitted.\n */\nexport class SelectionHandle {\n\n  constructor(group = null, extraInfo = null) {\n    this._eventRelay = new Events();\n    this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n    // Name of the group we're currently tracking, if any. Can change over time.\n    this._group = null;\n    // The Var we're currently tracking, if any. Can change over time.\n    this._var = null;\n    // The event handler subscription we currently have on var.on(\"change\").\n    this._varOnChangeSub = null;\n\n    this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n    this.setGroup(group);\n  }\n\n  /**\n   * Changes the Crosstalk group membership of this SelectionHandle. The group\n   * being switched away from (if any) will not have its selection value\n   * modified as a result of calling `setGroup`, even if this handle was the\n   * most recent handle to set the selection of the group.\n   *\n   * The group being switched to (if any) will also not have its selection value\n   * modified as a result of calling `setGroup`. If you want to set the\n   * selection value of the new group, call `set` explicitly.\n   *\n   * @param {string} group - The name of the Crosstalk group, or null (or\n   *   undefined) to clear the group.\n   */\n  setGroup(group) {\n    // If group is unchanged, do nothing\n    if (this._group === group)\n      return;\n    // Treat null, undefined, and other falsy values the same\n    if (!this._group && !group)\n      return;\n\n    if (this._var) {\n      this._var.off(\"change\", this._varOnChangeSub);\n      this._var = null;\n      this._varOnChangeSub = null;\n    }\n\n    this._group = group;\n\n    if (group) {\n      this._var = grp(group).var(\"selection\");\n      let sub = this._var.on(\"change\", (e) => {\n        this._eventRelay.trigger(\"change\", e, this);\n      });\n      this._varOnChangeSub = sub;\n    }\n  }\n\n  /**\n   * Retrieves the current selection for the group represented by this\n   * `SelectionHandle`.\n   *\n   * - If no selection is active, then this value will be falsy.\n   * - If a selection is active, but no data points are selected, then this\n   *   value will be an empty array.\n   * - If a selection is active, and data points are selected, then the keys\n   *   of the selected data points will be present in the array.\n   */\n  get value() {\n    return this._var ? this._var.get() : null;\n  }\n\n  /**\n   * Combines the given `extraInfo` (if any) with the handle's default\n   * `_extraInfo` (if any).\n   * @private\n   */\n  _mergeExtraInfo(extraInfo) {\n    // Important incidental effect: shallow clone is returned\n    return util.extend({},\n      this._extraInfo ? this._extraInfo : null,\n      extraInfo ? extraInfo : null);\n  }\n\n  /**\n   * Overwrites the current selection for the group, and raises the `\"change\"`\n   * event among all of the group's '`SelectionHandle` instances (including\n   * this one).\n   *\n   * @fires SelectionHandle#change\n   * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see\n   *   {@link SelectionHandle#value}).\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any options that were\n   *   passed into the `SelectionHandle` constructor).\n   */\n  set(selectedKeys, extraInfo) {\n    if (this._var)\n      this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));\n  }\n\n  /**\n   * Overwrites the current selection for the group, and raises the `\"change\"`\n   * event among all of the group's '`SelectionHandle` instances (including\n   * this one).\n   *\n   * @fires SelectionHandle#change\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any that were passed\n   *   into the `SelectionHandle` constructor).\n   */\n  clear(extraInfo) {\n    if (this._var)\n      this.set(void 0, this._mergeExtraInfo(extraInfo));\n  }\n\n  /**\n   * Subscribes to events on this `SelectionHandle`.\n   *\n   * @param {string} eventType - Indicates the type of events to listen to.\n   *   Currently, only `\"change\"` is supported.\n   * @param {SelectionHandle~listener} listener - The callback function that\n   *   will be invoked when the event occurs.\n   * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel\n   *   this subscription.\n   */\n  on(eventType, listener) {\n    return this._emitter.on(eventType, listener);\n  }\n\n  /**\n   * Cancels event subscriptions created by {@link SelectionHandle#on}.\n   *\n   * @param {string} eventType - The type of event to unsubscribe.\n   * @param {string|SelectionHandle~listener} listener - Either the callback\n   *   function previously passed into {@link SelectionHandle#on}, or the\n   *   string that was returned from {@link SelectionHandle#on}.\n   */\n  off(eventType, listener) {\n    return this._emitter.off(eventType, listener);\n  }\n\n  /**\n   * Shuts down the `SelectionHandle` object.\n   *\n   * Removes all event listeners that were added through this handle.\n   */\n  close() {\n    this._emitter.removeAllListeners();\n    this.setGroup(null);\n  }\n}\n\n/**\n * @callback SelectionHandle~listener\n * @param {Object} event - An object containing details of the event. For\n *   `\"change\"` events, this includes the properties `value` (the new\n *   value of the selection, or `undefined` if no selection is active),\n *   `oldValue` (the previous value of the selection), and `sender` (the\n *   `SelectionHandle` instance that made the change).\n */\n\n/**\n * @event SelectionHandle#change\n * @type {object}\n * @property {object} value - The new value of the selection, or `undefined`\n *   if no selection is active.\n * @property {object} oldValue - The previous value of the selection.\n * @property {SelectionHandle} sender - The `SelectionHandle` instance that\n *   changed the value.\n */\n",
+    "export function extend(target, ...sources) {\n  for (let i = 0; i < sources.length; i++) {\n    let src = sources[i];\n    if (typeof(src) === \"undefined\" || src === null)\n      continue;\n\n    for (let key in src) {\n      if (src.hasOwnProperty(key)) {\n        target[key] = src[key];\n      }\n    }\n  }\n  return target;\n}\n\nexport function checkSorted(list) {\n  for (let i = 1; i < list.length; i++) {\n    if (list[i] <= list[i-1]) {\n      throw new Error(\"List is not sorted or contains duplicate\");\n    }\n  }\n}\n\nexport function diffSortedLists(a, b) {\n  let i_a = 0;\n  let i_b = 0;\n\n  if (!a) a = [];\n  if (!b) b = [];\n\n  let a_only = [];\n  let b_only = [];\n\n  checkSorted(a);\n  checkSorted(b);\n\n  while (i_a < a.length && i_b < b.length) {\n    if (a[i_a] === b[i_b]) {\n      i_a++;\n      i_b++;\n    } else if (a[i_a] < b[i_b]) {\n      a_only.push(a[i_a++]);\n    } else {\n      b_only.push(b[i_b++]);\n    }\n  }\n\n  if (i_a < a.length)\n    a_only = a_only.concat(a.slice(i_a));\n  if (i_b < b.length)\n    b_only = b_only.concat(b.slice(i_b));\n  return {\n    removed: a_only,\n    added: b_only\n  };\n}\n\n// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }\n// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]\nexport function dataframeToD3(df) {\n  let names = [];\n  let length;\n  for (let name in df) {\n    if (df.hasOwnProperty(name))\n      names.push(name);\n    if (typeof(df[name]) !== \"object\" || typeof(df[name].length) === \"undefined\") {\n      throw new Error(\"All fields must be arrays\");\n    } else if (typeof(length) !== \"undefined\" && length !== df[name].length) {\n      throw new Error(\"All fields must be arrays of the same length\");\n    }\n    length = df[name].length;\n  }\n  let results = [];\n  let item;\n  for (let row = 0; row < length; row++) {\n    item = {};\n    for (let col = 0; col < names.length; col++) {\n      item[names[col]] = df[names[col]][row];\n    }\n    results.push(item);\n  }\n  return results;\n}\n\n/**\n * Keeps track of all event listener additions/removals and lets all active\n * listeners be removed with a single operation.\n *\n * @private\n */\nexport class SubscriptionTracker {\n  constructor(emitter) {\n    this._emitter = emitter;\n    this._subs = {};\n  }\n\n  on(eventType, listener) {\n    let sub = this._emitter.on(eventType, listener);\n    this._subs[sub] = eventType;\n    return sub;\n  }\n\n  off(eventType, listener) {\n    let sub = this._emitter.off(eventType, listener);\n    if (sub) {\n      delete this._subs[sub];\n    }\n    return sub;\n  }\n\n  removeAllListeners() {\n    let current_subs = this._subs;\n    this._subs = {};\n    Object.keys(current_subs).forEach((sub) => {\n      this._emitter.off(current_subs[sub], sub);\n    });\n  }\n}\n",
+    "import Events from \"./events\";\n\nexport default class Var {\n  constructor(group, name, /*optional*/ value) {\n    this._group = group;\n    this._name = name;\n    this._value = value;\n    this._events = new Events();\n  }\n\n  get() {\n    return this._value;\n  }\n\n  set(value, /*optional*/ event) {\n    if (this._value === value) {\n      // Do nothing; the value hasn't changed\n      return;\n    }\n    let oldValue = this._value;\n    this._value = value;\n    // Alert JavaScript listeners that the value has changed\n    let evt = {};\n    if (event && typeof(event) === \"object\") {\n      for (let k in event) {\n        if (event.hasOwnProperty(k))\n          evt[k] = event[k];\n      }\n    }\n    evt.oldValue = oldValue;\n    evt.value = value;\n    this._events.trigger(\"change\", evt, this);\n\n    // TODO: Make this extensible, to let arbitrary back-ends know that\n    // something has changed\n    if (global.Shiny && global.Shiny.onInputChange) {\n      global.Shiny.onInputChange(\n        \".clientValue-\" +\n          (this._group.name !== null ? this._group.name + \"-\" : \"\") +\n          this._name,\n        typeof(value) === \"undefined\" ? null : value\n      );\n    }\n  }\n\n  on(eventType, listener) {\n    return this._events.on(eventType, listener);\n  }\n\n  off(eventType, listener) {\n    return this._events.off(eventType, listener);\n  }\n}\n"
+  ]
+}
\ No newline at end of file
diff --git a/docs/articles/scFlow_files/crosstalk-1.2.1/js/crosstalk.min.js b/docs/articles/scFlow_files/crosstalk-1.2.1/js/crosstalk.min.js
new file mode 100644
index 0000000..b7ec0ac
--- /dev/null
+++ b/docs/articles/scFlow_files/crosstalk-1.2.1/js/crosstalk.min.js
@@ -0,0 +1,2 @@
+!function o(u,a,l){function s(n,e){if(!a[n]){if(!u[n]){var t="function"==typeof require&&require;if(!e&&t)return t(n,!0);if(f)return f(n,!0);var r=new Error("Cannot find module '"+n+"'");throw r.code="MODULE_NOT_FOUND",r}var i=a[n]={exports:{}};u[n][0].call(i.exports,function(e){var t=u[n][1][e];return s(t||e)},i,i.exports,o,u,a,l)}return a[n].exports}for(var f="function"==typeof require&&require,e=0;e?@[\\\]^`{|}~])/g,"\\$1")+"']"),r=JSON.parse(n[0].innerText),i=e.factory(t,r);o(t).data("crosstalk-instance",i),o(t).addClass("crosstalk-input-bound")}if(t.Shiny){var e=new t.Shiny.InputBinding,u=t.jQuery;u.extend(e,{find:function(e){return u(e).find(".crosstalk-input")},initialize:function(e){var t,n;u(e).hasClass("crosstalk-input-bound")||(n=o(t=e),Object.keys(r).forEach(function(e){n.hasClass(e)&&!n.hasClass("crosstalk-input-bound")&&i(r[e],t)}))},getId:function(e){return e.id},getValue:function(e){},setValue:function(e,t){},receiveMessage:function(e,t){},subscribe:function(e,t){u(e).data("crosstalk-instance").resume()},unsubscribe:function(e){u(e).data("crosstalk-instance").suspend()}}),t.Shiny.inputBindings.register(e,"crosstalk.inputBinding")}}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{}],7:[function(r,e,t){(function(e){"use strict";var t=function(e){{if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}}(r("./input")),n=r("./filter");var a=e.jQuery;t.register({className:"crosstalk-input-checkboxgroup",factory:function(e,r){var i=new n.FilterHandle(r.group),o=void 0,u=a(e);return u.on("change","input[type='checkbox']",function(){var e=u.find("input[type='checkbox']:checked");if(0===e.length)o=null,i.clear();else{var t={};e.each(function(){r.map[this.value].forEach(function(e){t[e]=!0})});var n=Object.keys(t);n.sort(),o=n,i.set(n)}}),{suspend:function(){i.clear()},resume:function(){o&&i.set(o)}}}})}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./input":6}],8:[function(r,e,t){(function(e){"use strict";var t=n(r("./input")),l=n(r("./util")),s=r("./filter");function n(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}var f=e.jQuery;t.register({className:"crosstalk-input-select",factory:function(e,n){var t=l.dataframeToD3(n.items),r={options:[{value:"",label:"(All)"}].concat(t),valueField:"value",labelField:"label",searchField:"label"},i=f(e).find("select")[0],o=f(i).selectize(r)[0].selectize,u=new s.FilterHandle(n.group),a=void 0;return o.on("change",function(){if(0===o.items.length)a=null,u.clear();else{var t={};o.items.forEach(function(e){n.map[e].forEach(function(e){t[e]=!0})});var e=Object.keys(t);e.sort(),a=e,u.set(e)}}),{suspend:function(){u.clear()},resume:function(){a&&u.set(a)}}}})}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./input":6,"./util":11}],9:[function(n,e,t){(function(e){"use strict";var d=function(e,t){if(Array.isArray(e))return e;if(Symbol.iterator in Object(e))return function(e,t){var n=[],r=!0,i=!1,o=void 0;try{for(var u,a=e[Symbol.iterator]();!(r=(u=a.next()).done)&&(n.push(u.value),!t||n.length!==t);r=!0);}catch(e){i=!0,o=e}finally{try{!r&&a.return&&a.return()}finally{if(i)throw o}}return n}(e,t);throw new TypeError("Invalid attempt to destructure non-iterable instance")},t=function(e){{if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}}(n("./input")),a=n("./filter");var v=e.jQuery,p=e.strftime;function y(e,t){for(var n=e.toString();n.length {\n        this._eventRelay.trigger(\"change\", e, this);\n      });\n      this._varOnChangeSub = sub;\n    }\n  }\n\n  /**\n   * Combine the given `extraInfo` (if any) with the handle's default\n   * `_extraInfo` (if any).\n   * @private\n   */\n  _mergeExtraInfo(extraInfo) {\n    return util.extend({},\n      this._extraInfo ? this._extraInfo : null,\n      extraInfo ? extraInfo : null);\n  }\n\n  /**\n   * Close the handle. This clears this handle's contribution to the filter set,\n   * and unsubscribes all event listeners.\n   */\n  close() {\n    this._emitter.removeAllListeners();\n    this.clear();\n    this.setGroup(null);\n  }\n\n  /**\n   * Clear this handle's contribution to the filter set.\n   *\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any options that were\n   *   passed into the `FilterHandle` constructor).\n   * \n   * @fires FilterHandle#change\n   */\n  clear(extraInfo) {\n    if (!this._filterSet)\n      return;\n    this._filterSet.clear(this._id);\n    this._onChange(extraInfo);\n  }\n\n  /**\n   * Set this handle's contribution to the filter set. This array should consist\n   * of the keys of the rows that _should_ be displayed; any keys that are not\n   * present in the array will be considered _filtered out_. Note that multiple\n   * `FilterHandle` instances in the group may each contribute an array of keys,\n   * and only those keys that appear in _all_ of the arrays make it through the\n   * filter.\n   *\n   * @param {string[]} keys - Empty array, or array of keys. To clear the\n   *   filter, don't pass an empty array; instead, use the\n   *   {@link FilterHandle#clear} method.\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any options that were\n   *   passed into the `FilterHandle` constructor).\n   * \n   * @fires FilterHandle#change\n   */\n  set(keys, extraInfo) {\n    if (!this._filterSet)\n      return;\n    this._filterSet.update(this._id, keys);\n    this._onChange(extraInfo);\n  }\n\n  /**\n   * @return {string[]|null} - Either: 1) an array of keys that made it through\n   *   all of the `FilterHandle` instances, or, 2) `null`, which means no filter\n   *   is being applied (all data should be displayed).\n   */\n  get filteredKeys() {\n    return this._filterSet ? this._filterSet.value : null;\n  }\n\n  /**\n   * Subscribe to events on this `FilterHandle`.\n   *\n   * @param {string} eventType - Indicates the type of events to listen to.\n   *   Currently, only `\"change\"` is supported.\n   * @param {FilterHandle~listener} listener - The callback function that\n   *   will be invoked when the event occurs.\n   * @return {string} - A token to pass to {@link FilterHandle#off} to cancel\n   *   this subscription.\n   */\n  on(eventType, listener) {\n    return this._emitter.on(eventType, listener);\n  }\n\n  /**\n   * Cancel event subscriptions created by {@link FilterHandle#on}.\n   *\n   * @param {string} eventType - The type of event to unsubscribe.\n   * @param {string|FilterHandle~listener} listener - Either the callback\n   *   function previously passed into {@link FilterHandle#on}, or the\n   *   string that was returned from {@link FilterHandle#on}.\n   */\n  off(eventType, listener) {\n    return this._emitter.off(eventType, listener);\n  }\n\n  _onChange(extraInfo) {\n    if (!this._filterSet)\n      return;\n    this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));\n  }\n\n  /**\n   * @callback FilterHandle~listener\n   * @param {Object} event - An object containing details of the event. For\n   *   `\"change\"` events, this includes the properties `value` (the new\n   *   value of the filter set, or `null` if no filter set is active),\n   *   `oldValue` (the previous value of the filter set), and `sender` (the\n   *   `FilterHandle` instance that made the change).\n   */\n\n}\n\n/**\n * @event FilterHandle#change\n * @type {object}\n * @property {object} value - The new value of the filter set, or `null`\n *   if no filter set is active.\n * @property {object} oldValue - The previous value of the filter set.\n * @property {FilterHandle} sender - The `FilterHandle` instance that\n *   changed the value.\n */\n","import { diffSortedLists } from \"./util\";\n\nfunction naturalComparator(a, b) {\n  if (a === b) {\n    return 0;\n  } else if (a < b) {\n    return -1;\n  } else if (a > b) {\n    return 1;\n  }\n}\n\n/**\n * @private\n */\nexport default class FilterSet {\n  constructor() {\n    this.reset();\n  }\n\n  reset() {\n    // Key: handle ID, Value: array of selected keys, or null\n    this._handles = {};\n    // Key: key string, Value: count of handles that include it\n    this._keys = {};\n    this._value = null;\n    this._activeHandles = 0;\n  }\n\n  get value() {\n    return this._value;\n  }\n\n  update(handleId, keys) {\n    if (keys !== null) {\n      keys = keys.slice(0); // clone before sorting\n      keys.sort(naturalComparator);\n    }\n\n    let {added, removed} = diffSortedLists(this._handles[handleId], keys);\n    this._handles[handleId] = keys;\n\n    for (let i = 0; i < added.length; i++) {\n      this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;\n    }\n    for (let i = 0; i < removed.length; i++) {\n      this._keys[removed[i]]--;\n    }\n\n    this._updateValue(keys);\n  }\n\n  /**\n   * @param {string[]} keys Sorted array of strings that indicate\n   * a superset of possible keys.\n   * @private\n   */\n  _updateValue(keys = this._allKeys) {\n    let handleCount = Object.keys(this._handles).length;\n    if (handleCount === 0) {\n      this._value = null;\n    } else {\n      this._value = [];\n      for (let i = 0; i < keys.length; i++) {\n        let count = this._keys[keys[i]];\n        if (count === handleCount) {\n          this._value.push(keys[i]);\n        }\n      }\n    }\n  }\n\n  clear(handleId) {\n    if (typeof(this._handles[handleId]) === \"undefined\") {\n      return;\n    }\n\n    let keys = this._handles[handleId];\n    if (!keys) {\n      keys = [];\n    }\n\n    for (let i = 0; i < keys.length; i++) {\n      this._keys[keys[i]]--;\n    }\n    delete this._handles[handleId];\n\n    this._updateValue();\n  }\n\n  get _allKeys() {\n    let allKeys = Object.keys(this._keys);\n    allKeys.sort(naturalComparator);\n    return allKeys;\n  }\n}\n","import Var from \"./var\";\n\n// Use a global so that multiple copies of crosstalk.js can be loaded and still\n// have groups behave as singletons across all copies.\nglobal.__crosstalk_groups = global.__crosstalk_groups || {};\nlet groups = global.__crosstalk_groups;\n\nexport default function group(groupName) {\n  if (groupName && typeof(groupName) === \"string\") {\n    if (!groups.hasOwnProperty(groupName)) {\n      groups[groupName] = new Group(groupName);\n    }\n    return groups[groupName];\n  } else if (typeof(groupName) === \"object\" && groupName._vars && groupName.var) {\n    // Appears to already be a group object\n    return groupName;\n  } else if (Array.isArray(groupName) &&\n      groupName.length == 1 &&\n      typeof(groupName[0]) === \"string\") {\n    return group(groupName[0]);\n  } else {\n    throw new Error(\"Invalid groupName argument\");\n  }\n}\n\nclass Group {\n  constructor(name) {\n    this.name = name;\n    this._vars = {};\n  }\n\n  var(name) {\n    if (!name || typeof(name) !== \"string\") {\n      throw new Error(\"Invalid var name\");\n    }\n\n    if (!this._vars.hasOwnProperty(name))\n      this._vars[name] = new Var(this, name);\n    return this._vars[name];\n  }\n\n  has(name) {\n    if (!name || typeof(name) !== \"string\") {\n      throw new Error(\"Invalid var name\");\n    }\n\n    return this._vars.hasOwnProperty(name);\n  }\n}\n","import group from \"./group\";\nimport { SelectionHandle } from \"./selection\";\nimport { FilterHandle } from \"./filter\";\nimport { bind } from \"./input\";\nimport \"./input_selectize\";\nimport \"./input_checkboxgroup\";\nimport \"./input_slider\";\n\nconst defaultGroup = group(\"default\");\n\nfunction var_(name) {\n  return defaultGroup.var(name);\n}\n\nfunction has(name) {\n  return defaultGroup.has(name);\n}\n\nif (global.Shiny) {\n  global.Shiny.addCustomMessageHandler(\"update-client-value\", function(message) {\n    if (typeof(message.group) === \"string\") {\n      group(message.group).var(message.name).set(message.value);\n    } else {\n      var_(message.name).set(message.value);\n    }\n  });\n}\n\nconst crosstalk = {\n  group: group,\n  var: var_,\n  has: has,\n  SelectionHandle: SelectionHandle,\n  FilterHandle: FilterHandle,\n  bind: bind\n};\n\n/**\n * @namespace crosstalk\n */\nexport default crosstalk;\nglobal.crosstalk = crosstalk;\n","let $ = global.jQuery;\n\nlet bindings = {};\n\nexport function register(reg) {\n  bindings[reg.className] = reg;\n  if (global.document && global.document.readyState !== \"complete\") {\n    $(() => {\n      bind();\n    });\n  } else if (global.document) {\n    setTimeout(bind, 100);\n  }\n}\n\nexport function bind() {\n  Object.keys(bindings).forEach(function(className) {\n    let binding = bindings[className];\n    $(\".\" + binding.className).not(\".crosstalk-input-bound\").each(function(i, el) {\n      bindInstance(binding, el);\n    });\n  });\n}\n\n// Escape jQuery identifier\nfunction $escape(val) {\n  return val.replace(/([!\"#$%&'()*+,./:;<=>?@[\\\\\\]^`{|}~])/g, \"\\\\$1\");\n}\n\nfunction bindEl(el) {\n  let $el = $(el);\n  Object.keys(bindings).forEach(function(className) {\n    if ($el.hasClass(className) && !$el.hasClass(\"crosstalk-input-bound\")) {\n      let binding = bindings[className];\n      bindInstance(binding, el);\n    }\n  });\n}\n\nfunction bindInstance(binding, el) {\n  let jsonEl = $(el).find(\"script[type='application/json'][data-for='\" + $escape(el.id) + \"']\");\n  let data = JSON.parse(jsonEl[0].innerText);\n\n  let instance = binding.factory(el, data);\n  $(el).data(\"crosstalk-instance\", instance);\n  $(el).addClass(\"crosstalk-input-bound\");\n}\n\nif (global.Shiny) {\n  let inputBinding = new global.Shiny.InputBinding();\n  let $ = global.jQuery;\n  $.extend(inputBinding, {\n    find: function(scope) {\n      return $(scope).find(\".crosstalk-input\");\n    },\n    initialize: function(el) {\n      if (!$(el).hasClass(\"crosstalk-input-bound\")) {\n        bindEl(el);\n      }\n    },\n    getId: function(el) {\n      return el.id;\n    },\n    getValue: function(el) {\n\n    },\n    setValue: function(el, value) {\n\n    },\n    receiveMessage: function(el, data) {\n\n    },\n    subscribe: function(el, callback) {\n      $(el).data(\"crosstalk-instance\").resume();\n    },\n    unsubscribe: function(el) {\n      $(el).data(\"crosstalk-instance\").suspend();\n    }\n  });\n  global.Shiny.inputBindings.register(inputBinding, \"crosstalk.inputBinding\");\n}\n","import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n  className: \"crosstalk-input-checkboxgroup\",\n\n  factory: function(el, data) {\n    /*\n     * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n     * group: \"ct-groupname\"\n     */\n    let ctHandle = new FilterHandle(data.group);\n\n    let lastKnownKeys;\n    let $el = $(el);\n    $el.on(\"change\", \"input[type='checkbox']\", function() {\n      let checked = $el.find(\"input[type='checkbox']:checked\");\n      if (checked.length === 0) {\n        lastKnownKeys = null;\n        ctHandle.clear();\n      } else {\n        let keys = {};\n        checked.each(function() {\n          data.map[this.value].forEach(function(key) {\n            keys[key] = true;\n          });\n        });\n        let keyArray = Object.keys(keys);\n        keyArray.sort();\n        lastKnownKeys = keyArray;\n        ctHandle.set(keyArray);\n      }\n    });\n\n    return {\n      suspend: function() {\n        ctHandle.clear();\n      },\n      resume: function() {\n        if (lastKnownKeys)\n          ctHandle.set(lastKnownKeys);\n      }\n    };\n  }\n});\n","import * as input from \"./input\";\nimport * as util from \"./util\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n  className: \"crosstalk-input-select\",\n\n  factory: function(el, data) {\n    /*\n     * items: {value: [...], label: [...]}\n     * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n     * group: \"ct-groupname\"\n     */\n\n    let first = [{value: \"\", label: \"(All)\"}];\n    let items = util.dataframeToD3(data.items);\n    let opts = {\n      options: first.concat(items),\n      valueField: \"value\",\n      labelField: \"label\",\n      searchField: \"label\"\n    };\n\n    let select = $(el).find(\"select\")[0];\n\n    let selectize = $(select).selectize(opts)[0].selectize;\n\n    let ctHandle = new FilterHandle(data.group);\n\n    let lastKnownKeys;\n    selectize.on(\"change\", function() {\n      if (selectize.items.length === 0) {\n        lastKnownKeys = null;\n        ctHandle.clear();\n      } else {\n        let keys = {};\n        selectize.items.forEach(function(group) {\n          data.map[group].forEach(function(key) {\n            keys[key] = true;\n          });\n        });\n        let keyArray = Object.keys(keys);\n        keyArray.sort();\n        lastKnownKeys = keyArray;\n        ctHandle.set(keyArray);\n      }\n    });\n\n    return {\n      suspend: function() {\n        ctHandle.clear();\n      },\n      resume: function() {\n        if (lastKnownKeys)\n          ctHandle.set(lastKnownKeys);\n      }\n    };\n  }\n});\n","import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\nlet strftime = global.strftime;\n\ninput.register({\n  className: \"crosstalk-input-slider\",\n\n  factory: function(el, data) {\n    /*\n     * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n     * group: \"ct-groupname\"\n     */\n    let ctHandle = new FilterHandle(data.group);\n\n    let opts = {};\n    let $el = $(el).find(\"input\");\n    let dataType = $el.data(\"data-type\");\n    let timeFormat = $el.data(\"time-format\");\n    let round = $el.data(\"round\");\n    let timeFormatter;\n\n    // Set up formatting functions\n    if (dataType === \"date\") {\n      timeFormatter = strftime.utc();\n      opts.prettify = function(num) {\n        return timeFormatter(timeFormat, new Date(num));\n      };\n\n    } else if (dataType === \"datetime\") {\n      let timezone = $el.data(\"timezone\");\n      if (timezone)\n        timeFormatter = strftime.timezone(timezone);\n      else\n        timeFormatter = strftime;\n\n      opts.prettify = function(num) {\n        return timeFormatter(timeFormat, new Date(num));\n      };\n    } else if (dataType === \"number\") {\n      if (typeof round !== \"undefined\")\n        opts.prettify = function(num) {\n          let factor = Math.pow(10, round);\n          return Math.round(num * factor) / factor;\n        };\n    }\n\n    $el.ionRangeSlider(opts);\n\n    function getValue() {\n      let result = $el.data(\"ionRangeSlider\").result;\n\n      // Function for converting numeric value from slider to appropriate type.\n      let convert;\n      let dataType = $el.data(\"data-type\");\n      if (dataType === \"date\") {\n        convert = function(val) {\n          return formatDateUTC(new Date(+val));\n        };\n      } else if (dataType === \"datetime\") {\n        convert = function(val) {\n          // Convert ms to s\n          return +val / 1000;\n        };\n      } else {\n        convert = function(val) { return +val; };\n      }\n\n      if ($el.data(\"ionRangeSlider\").options.type === \"double\") {\n        return [convert(result.from), convert(result.to)];\n      } else {\n        return convert(result.from);\n      }\n    }\n\n    let lastKnownKeys = null;\n\n    $el.on(\"change.crosstalkSliderInput\", function(event) {\n      if (!$el.data(\"updating\") && !$el.data(\"animating\")) {\n        let [from, to] = getValue();\n        let keys = [];\n        for (let i = 0; i < data.values.length; i++) {\n          let val = data.values[i];\n          if (val >= from && val <= to) {\n            keys.push(data.keys[i]);\n          }\n        }\n        keys.sort();\n        ctHandle.set(keys);\n        lastKnownKeys = keys;\n      }\n    });\n\n\n    // let $el = $(el);\n    // $el.on(\"change\", \"input[type=\"checkbox\"]\", function() {\n    //   let checked = $el.find(\"input[type=\"checkbox\"]:checked\");\n    //   if (checked.length === 0) {\n    //     ctHandle.clear();\n    //   } else {\n    //     let keys = {};\n    //     checked.each(function() {\n    //       data.map[this.value].forEach(function(key) {\n    //         keys[key] = true;\n    //       });\n    //     });\n    //     let keyArray = Object.keys(keys);\n    //     keyArray.sort();\n    //     ctHandle.set(keyArray);\n    //   }\n    // });\n\n    return {\n      suspend: function() {\n        ctHandle.clear();\n      },\n      resume: function() {\n        if (lastKnownKeys)\n          ctHandle.set(lastKnownKeys);\n      }\n    };\n  }\n});\n\n\n// Convert a number to a string with leading zeros\nfunction padZeros(n, digits) {\n  let str = n.toString();\n  while (str.length < digits)\n    str = \"0\" + str;\n  return str;\n}\n\n// Given a Date object, return a string in yyyy-mm-dd format, using the\n// UTC date. This may be a day off from the date in the local time zone.\nfunction formatDateUTC(date) {\n  if (date instanceof Date) {\n    return date.getUTCFullYear() + \"-\" +\n           padZeros(date.getUTCMonth()+1, 2) + \"-\" +\n           padZeros(date.getUTCDate(), 2);\n\n  } else {\n    return null;\n  }\n}\n","import Events from \"./events\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\n/**\n * Use this class to read and write (and listen for changes to) the selection\n * for a Crosstalk group. This is intended to be used for linked brushing.\n *\n * If two (or more) `SelectionHandle` instances in the same webpage share the\n * same group name, they will share the same state. Setting the selection using\n * one `SelectionHandle` instance will result in the `value` property instantly\n * changing across the others, and `\"change\"` event listeners on all instances\n * (including the one that initiated the sending) will fire.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n *   null or undefined (or any other falsy value). This can be changed later\n *   via the [SelectionHandle#setGroup](#setGroup) method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n *   the event object whenever an event is emitted.\n */\nexport class SelectionHandle {\n\n  constructor(group = null, extraInfo = null) {\n    this._eventRelay = new Events();\n    this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n    // Name of the group we're currently tracking, if any. Can change over time.\n    this._group = null;\n    // The Var we're currently tracking, if any. Can change over time.\n    this._var = null;\n    // The event handler subscription we currently have on var.on(\"change\").\n    this._varOnChangeSub = null;\n\n    this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n    this.setGroup(group);\n  }\n\n  /**\n   * Changes the Crosstalk group membership of this SelectionHandle. The group\n   * being switched away from (if any) will not have its selection value\n   * modified as a result of calling `setGroup`, even if this handle was the\n   * most recent handle to set the selection of the group.\n   *\n   * The group being switched to (if any) will also not have its selection value\n   * modified as a result of calling `setGroup`. If you want to set the\n   * selection value of the new group, call `set` explicitly.\n   *\n   * @param {string} group - The name of the Crosstalk group, or null (or\n   *   undefined) to clear the group.\n   */\n  setGroup(group) {\n    // If group is unchanged, do nothing\n    if (this._group === group)\n      return;\n    // Treat null, undefined, and other falsy values the same\n    if (!this._group && !group)\n      return;\n\n    if (this._var) {\n      this._var.off(\"change\", this._varOnChangeSub);\n      this._var = null;\n      this._varOnChangeSub = null;\n    }\n\n    this._group = group;\n\n    if (group) {\n      this._var = grp(group).var(\"selection\");\n      let sub = this._var.on(\"change\", (e) => {\n        this._eventRelay.trigger(\"change\", e, this);\n      });\n      this._varOnChangeSub = sub;\n    }\n  }\n\n  /**\n   * Retrieves the current selection for the group represented by this\n   * `SelectionHandle`.\n   *\n   * - If no selection is active, then this value will be falsy.\n   * - If a selection is active, but no data points are selected, then this\n   *   value will be an empty array.\n   * - If a selection is active, and data points are selected, then the keys\n   *   of the selected data points will be present in the array.\n   */\n  get value() {\n    return this._var ? this._var.get() : null;\n  }\n\n  /**\n   * Combines the given `extraInfo` (if any) with the handle's default\n   * `_extraInfo` (if any).\n   * @private\n   */\n  _mergeExtraInfo(extraInfo) {\n    // Important incidental effect: shallow clone is returned\n    return util.extend({},\n      this._extraInfo ? this._extraInfo : null,\n      extraInfo ? extraInfo : null);\n  }\n\n  /**\n   * Overwrites the current selection for the group, and raises the `\"change\"`\n   * event among all of the group's '`SelectionHandle` instances (including\n   * this one).\n   *\n   * @fires SelectionHandle#change\n   * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see\n   *   {@link SelectionHandle#value}).\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any options that were\n   *   passed into the `SelectionHandle` constructor).\n   */\n  set(selectedKeys, extraInfo) {\n    if (this._var)\n      this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));\n  }\n\n  /**\n   * Overwrites the current selection for the group, and raises the `\"change\"`\n   * event among all of the group's '`SelectionHandle` instances (including\n   * this one).\n   *\n   * @fires SelectionHandle#change\n   * @param {Object} [extraInfo] - Extra properties to be included on the event\n   *   object that's passed to listeners (in addition to any that were passed\n   *   into the `SelectionHandle` constructor).\n   */\n  clear(extraInfo) {\n    if (this._var)\n      this.set(void 0, this._mergeExtraInfo(extraInfo));\n  }\n\n  /**\n   * Subscribes to events on this `SelectionHandle`.\n   *\n   * @param {string} eventType - Indicates the type of events to listen to.\n   *   Currently, only `\"change\"` is supported.\n   * @param {SelectionHandle~listener} listener - The callback function that\n   *   will be invoked when the event occurs.\n   * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel\n   *   this subscription.\n   */\n  on(eventType, listener) {\n    return this._emitter.on(eventType, listener);\n  }\n\n  /**\n   * Cancels event subscriptions created by {@link SelectionHandle#on}.\n   *\n   * @param {string} eventType - The type of event to unsubscribe.\n   * @param {string|SelectionHandle~listener} listener - Either the callback\n   *   function previously passed into {@link SelectionHandle#on}, or the\n   *   string that was returned from {@link SelectionHandle#on}.\n   */\n  off(eventType, listener) {\n    return this._emitter.off(eventType, listener);\n  }\n\n  /**\n   * Shuts down the `SelectionHandle` object.\n   *\n   * Removes all event listeners that were added through this handle.\n   */\n  close() {\n    this._emitter.removeAllListeners();\n    this.setGroup(null);\n  }\n}\n\n/**\n * @callback SelectionHandle~listener\n * @param {Object} event - An object containing details of the event. For\n *   `\"change\"` events, this includes the properties `value` (the new\n *   value of the selection, or `undefined` if no selection is active),\n *   `oldValue` (the previous value of the selection), and `sender` (the\n *   `SelectionHandle` instance that made the change).\n */\n\n/**\n * @event SelectionHandle#change\n * @type {object}\n * @property {object} value - The new value of the selection, or `undefined`\n *   if no selection is active.\n * @property {object} oldValue - The previous value of the selection.\n * @property {SelectionHandle} sender - The `SelectionHandle` instance that\n *   changed the value.\n */\n","export function extend(target, ...sources) {\n  for (let i = 0; i < sources.length; i++) {\n    let src = sources[i];\n    if (typeof(src) === \"undefined\" || src === null)\n      continue;\n\n    for (let key in src) {\n      if (src.hasOwnProperty(key)) {\n        target[key] = src[key];\n      }\n    }\n  }\n  return target;\n}\n\nexport function checkSorted(list) {\n  for (let i = 1; i < list.length; i++) {\n    if (list[i] <= list[i-1]) {\n      throw new Error(\"List is not sorted or contains duplicate\");\n    }\n  }\n}\n\nexport function diffSortedLists(a, b) {\n  let i_a = 0;\n  let i_b = 0;\n\n  if (!a) a = [];\n  if (!b) b = [];\n\n  let a_only = [];\n  let b_only = [];\n\n  checkSorted(a);\n  checkSorted(b);\n\n  while (i_a < a.length && i_b < b.length) {\n    if (a[i_a] === b[i_b]) {\n      i_a++;\n      i_b++;\n    } else if (a[i_a] < b[i_b]) {\n      a_only.push(a[i_a++]);\n    } else {\n      b_only.push(b[i_b++]);\n    }\n  }\n\n  if (i_a < a.length)\n    a_only = a_only.concat(a.slice(i_a));\n  if (i_b < b.length)\n    b_only = b_only.concat(b.slice(i_b));\n  return {\n    removed: a_only,\n    added: b_only\n  };\n}\n\n// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }\n// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]\nexport function dataframeToD3(df) {\n  let names = [];\n  let length;\n  for (let name in df) {\n    if (df.hasOwnProperty(name))\n      names.push(name);\n    if (typeof(df[name]) !== \"object\" || typeof(df[name].length) === \"undefined\") {\n      throw new Error(\"All fields must be arrays\");\n    } else if (typeof(length) !== \"undefined\" && length !== df[name].length) {\n      throw new Error(\"All fields must be arrays of the same length\");\n    }\n    length = df[name].length;\n  }\n  let results = [];\n  let item;\n  for (let row = 0; row < length; row++) {\n    item = {};\n    for (let col = 0; col < names.length; col++) {\n      item[names[col]] = df[names[col]][row];\n    }\n    results.push(item);\n  }\n  return results;\n}\n\n/**\n * Keeps track of all event listener additions/removals and lets all active\n * listeners be removed with a single operation.\n *\n * @private\n */\nexport class SubscriptionTracker {\n  constructor(emitter) {\n    this._emitter = emitter;\n    this._subs = {};\n  }\n\n  on(eventType, listener) {\n    let sub = this._emitter.on(eventType, listener);\n    this._subs[sub] = eventType;\n    return sub;\n  }\n\n  off(eventType, listener) {\n    let sub = this._emitter.off(eventType, listener);\n    if (sub) {\n      delete this._subs[sub];\n    }\n    return sub;\n  }\n\n  removeAllListeners() {\n    let current_subs = this._subs;\n    this._subs = {};\n    Object.keys(current_subs).forEach((sub) => {\n      this._emitter.off(current_subs[sub], sub);\n    });\n  }\n}\n","import Events from \"./events\";\n\nexport default class Var {\n  constructor(group, name, /*optional*/ value) {\n    this._group = group;\n    this._name = name;\n    this._value = value;\n    this._events = new Events();\n  }\n\n  get() {\n    return this._value;\n  }\n\n  set(value, /*optional*/ event) {\n    if (this._value === value) {\n      // Do nothing; the value hasn't changed\n      return;\n    }\n    let oldValue = this._value;\n    this._value = value;\n    // Alert JavaScript listeners that the value has changed\n    let evt = {};\n    if (event && typeof(event) === \"object\") {\n      for (let k in event) {\n        if (event.hasOwnProperty(k))\n          evt[k] = event[k];\n      }\n    }\n    evt.oldValue = oldValue;\n    evt.value = value;\n    this._events.trigger(\"change\", evt, this);\n\n    // TODO: Make this extensible, to let arbitrary back-ends know that\n    // something has changed\n    if (global.Shiny && global.Shiny.onInputChange) {\n      global.Shiny.onInputChange(\n        \".clientValue-\" +\n          (this._group.name !== null ? this._group.name + \"-\" : \"\") +\n          this._name,\n        typeof(value) === \"undefined\" ? null : value\n      );\n    }\n  }\n\n  on(eventType, listener) {\n    return this._events.on(eventType, listener);\n  }\n\n  off(eventType, listener) {\n    return this._events.off(eventType, listener);\n  }\n}\n"]}
\ No newline at end of file
diff --git a/docs/articles/scFlow_files/crosstalk-1.2.1/scss/crosstalk.scss b/docs/articles/scFlow_files/crosstalk-1.2.1/scss/crosstalk.scss
new file mode 100644
index 0000000..3566561
--- /dev/null
+++ b/docs/articles/scFlow_files/crosstalk-1.2.1/scss/crosstalk.scss
@@ -0,0 +1,75 @@
+/* Adjust margins outwards, so column contents line up with the edges of the
+   parent of container-fluid. */
+.container-fluid.crosstalk-bscols {
+  margin-left: -30px;
+  margin-right: -30px;
+  white-space: normal;
+}
+
+/* But don't adjust the margins outwards if we're directly under the body,
+   i.e. we were the top-level of something at the console. */
+body > .container-fluid.crosstalk-bscols {
+  margin-left: auto;
+  margin-right: auto;
+}
+
+.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column {
+  display: inline-block;
+  padding-right: 12px;
+  vertical-align: top;
+}
+
+@media only screen and (max-width:480px) {
+  .crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column {
+    display: block;
+    padding-right: inherit;
+  }
+}
+
+/* Relevant BS3 styles to make filter_checkbox() look reasonable without Bootstrap */
+.crosstalk-input {
+  margin-bottom: 15px; /* a la .form-group */
+  .control-label {
+    margin-bottom: 0;
+    vertical-align: middle;
+  }
+  input[type="checkbox"] {
+    margin: 4px 0 0;
+    margin-top: 1px;
+    line-height: normal;
+  }
+  .checkbox {
+    position: relative;
+    display: block;
+    margin-top: 10px;
+    margin-bottom: 10px;
+  }
+  .checkbox > label{
+    padding-left: 20px;
+    margin-bottom: 0;
+    font-weight: 400;
+    cursor: pointer;
+  }
+  .checkbox input[type="checkbox"],
+  .checkbox-inline input[type="checkbox"] {
+    position: absolute;
+    margin-top: 2px;
+    margin-left: -20px;
+  }
+  .checkbox + .checkbox {
+    margin-top: -5px;
+  }
+  .checkbox-inline {
+    position: relative;
+    display: inline-block;
+    padding-left: 20px;
+    margin-bottom: 0;
+    font-weight: 400;
+    vertical-align: middle;
+    cursor: pointer;
+  }
+  .checkbox-inline + .checkbox-inline {
+    margin-top: 0;
+    margin-left: 10px;
+  }
+}
diff --git a/docs/articles/scFlow_files/datatables-binding-0.31/datatables.js b/docs/articles/scFlow_files/datatables-binding-0.31/datatables.js
new file mode 100644
index 0000000..d21dff0
--- /dev/null
+++ b/docs/articles/scFlow_files/datatables-binding-0.31/datatables.js
@@ -0,0 +1,1519 @@
+(function() {
+
+// some helper functions: using a global object DTWidget so that it can be used
+// in JS() code, e.g. datatable(options = list(foo = JS('code'))); unlike R's
+// dynamic scoping, when 'code' is eval'ed, JavaScript does not know objects
+// from the "parent frame", e.g. JS('DTWidget') will not work unless it was made
+// a global object
+var DTWidget = {};
+
+// 123456666.7890 -> 123,456,666.7890
+var markInterval = function(d, digits, interval, mark, decMark, precision) {
+  x = precision ? d.toPrecision(digits) : d.toFixed(digits);
+  if (!/^-?[\d.]+$/.test(x)) return x;
+  var xv = x.split('.');
+  if (xv.length > 2) return x;  // should have at most one decimal point
+  xv[0] = xv[0].replace(new RegExp('\\B(?=(\\d{' + interval + '})+(?!\\d))', 'g'), mark);
+  return xv.join(decMark);
+};
+
+DTWidget.formatCurrency = function(data, currency, digits, interval, mark, decMark, before, zeroPrint) {
+  var d = parseFloat(data);
+  if (isNaN(d)) return '';
+  if (zeroPrint !== null && d === 0.0) return zeroPrint;
+  var res = markInterval(d, digits, interval, mark, decMark);
+  res = before ? (/^-/.test(res) ? '-' + currency + res.replace(/^-/, '') : currency + res) :
+    res + currency;
+  return res;
+};
+
+DTWidget.formatString = function(data, prefix, suffix) {
+  var d = data;
+  if (d === null) return '';
+  return prefix + d + suffix;
+};
+
+DTWidget.formatPercentage = function(data, digits, interval, mark, decMark, zeroPrint) {
+  var d = parseFloat(data);
+  if (isNaN(d)) return '';
+  if (zeroPrint !== null && d === 0.0) return zeroPrint;
+  return markInterval(d * 100, digits, interval, mark, decMark) + '%';
+};
+
+DTWidget.formatRound = function(data, digits, interval, mark, decMark, zeroPrint) {
+  var d = parseFloat(data);
+  if (isNaN(d)) return '';
+  if (zeroPrint !== null && d === 0.0) return zeroPrint;
+  return markInterval(d, digits, interval, mark, decMark);
+};
+
+DTWidget.formatSignif = function(data, digits, interval, mark, decMark, zeroPrint) {
+  var d = parseFloat(data);
+  if (isNaN(d)) return '';
+  if (zeroPrint !== null && d === 0.0) return zeroPrint;
+  return markInterval(d, digits, interval, mark, decMark, true);
+};
+
+DTWidget.formatDate = function(data, method, params) {
+  var d = data;
+  if (d === null) return '';
+  // (new Date('2015-10-28')).toDateString() may return 2015-10-27 because the
+  // actual time created could be like 'Tue Oct 27 2015 19:00:00 GMT-0500 (CDT)',
+  // i.e. the date-only string is treated as UTC time instead of local time
+  if ((method === 'toDateString' || method === 'toLocaleDateString') && /^\d{4,}\D\d{2}\D\d{2}$/.test(d)) {
+    d = d.split(/\D/);
+    d = new Date(d[0], d[1] - 1, d[2]);
+  } else {
+    d = new Date(d);
+  }
+  return d[method].apply(d, params);
+};
+
+window.DTWidget = DTWidget;
+
+// A helper function to update the properties of existing filters
+var setFilterProps = function(td, props) {
+  // Update enabled/disabled state
+  var $input = $(td).find('input').first();
+  var searchable = $input.data('searchable');
+  $input.prop('disabled', !searchable || props.disabled);
+
+  // Based on the filter type, set its new values
+  var type = td.getAttribute('data-type');
+  if (['factor', 'logical'].includes(type)) {
+    // Reformat the new dropdown options for use with selectize
+    var new_vals = props.params.options.map(function(item) {
+      return { text: item, value: item };
+    });
+
+    // Find the selectize object
+    var dropdown = $(td).find('.selectized').eq(0)[0].selectize;
+
+    // Note the current values
+    var old_vals = dropdown.getValue();
+
+    // Remove the existing values
+    dropdown.clearOptions();
+
+    // Add the new options
+    dropdown.addOption(new_vals);
+
+    // Preserve the existing values
+    dropdown.setValue(old_vals);
+
+  } else if (['number', 'integer', 'date', 'time'].includes(type)) {
+    // Apply internal scaling to new limits. Updating scale not yet implemented.
+    var slider = $(td).find('.noUi-target').eq(0);
+    var scale = Math.pow(10, Math.max(0, +slider.data('scale') || 0));
+    var new_vals = [props.params.min * scale, props.params.max * scale];
+
+    // Note what the new limits will be just for this filter
+    var new_lims = new_vals.slice();
+
+    // Determine the current values and limits
+    var old_vals = slider.val().map(Number);
+    var old_lims = slider.noUiSlider('options').range;
+    old_lims = [old_lims.min, old_lims.max];
+
+    // Preserve the current values if filters have been applied; otherwise, apply no filtering
+    if (old_vals[0] != old_lims[0]) {
+      new_vals[0] = Math.max(old_vals[0], new_vals[0]);
+    }
+
+    if (old_vals[1] != old_lims[1]) {
+      new_vals[1] = Math.min(old_vals[1], new_vals[1]);
+    }
+
+    // Update the endpoints of the slider
+    slider.noUiSlider({
+      start: new_vals,
+      range: {'min': new_lims[0], 'max': new_lims[1]}
+    }, true);
+  }
+};
+
+var transposeArray2D = function(a) {
+  return a.length === 0 ? a : HTMLWidgets.transposeArray2D(a);
+};
+
+var crosstalkPluginsInstalled = false;
+
+function maybeInstallCrosstalkPlugins() {
+  if (crosstalkPluginsInstalled)
+    return;
+  crosstalkPluginsInstalled = true;
+
+  $.fn.dataTable.ext.afnFiltering.push(
+    function(oSettings, aData, iDataIndex) {
+      var ctfilter = oSettings.nTable.ctfilter;
+      if (ctfilter && !ctfilter[iDataIndex])
+        return false;
+
+      var ctselect = oSettings.nTable.ctselect;
+      if (ctselect && !ctselect[iDataIndex])
+        return false;
+
+      return true;
+    }
+  );
+}
+
+HTMLWidgets.widget({
+  name: "datatables",
+  type: "output",
+  renderOnNullValue: true,
+  initialize: function(el, width, height) {
+    // in order that the type=number inputs return a number
+    $.valHooks.number = {
+      get: function(el) {
+        var value = parseFloat(el.value);
+        return isNaN(value) ? "" : value;
+      }
+    };
+    $(el).html(' ');
+    return {
+      data: null,
+      ctfilterHandle: new crosstalk.FilterHandle(),
+      ctfilterSubscription: null,
+      ctselectHandle: new crosstalk.SelectionHandle(),
+      ctselectSubscription: null
+    };
+  },
+  renderValue: function(el, data, instance) {
+    if (el.offsetWidth === 0 || el.offsetHeight === 0) {
+      instance.data = data;
+      return;
+    }
+    instance.data = null;
+    var $el = $(el);
+    $el.empty();
+
+    if (data === null) {
+      $el.append(' ');
+      // clear previous Shiny inputs (if any)
+      for (var i in instance.clearInputs) instance.clearInputs[i]();
+      instance.clearInputs = {};
+      return;
+    }
+
+    var crosstalkOptions = data.crosstalkOptions;
+    if (!crosstalkOptions) crosstalkOptions = {
+      'key': null, 'group': null
+    };
+    if (crosstalkOptions.group) {
+      maybeInstallCrosstalkPlugins();
+      instance.ctfilterHandle.setGroup(crosstalkOptions.group);
+      instance.ctselectHandle.setGroup(crosstalkOptions.group);
+    }
+
+    // if we are in the viewer then we always want to fillContainer and
+    // and autoHideNavigation (unless the user has explicitly set these)
+    if (window.HTMLWidgets.viewerMode) {
+      if (!data.hasOwnProperty("fillContainer"))
+        data.fillContainer = true;
+      if (!data.hasOwnProperty("autoHideNavigation"))
+        data.autoHideNavigation = true;
+    }
+
+    // propagate fillContainer to instance (so we have it in resize)
+    instance.fillContainer = data.fillContainer;
+
+    var cells = data.data;
+
+    if (cells instanceof Array) cells = transposeArray2D(cells);
+
+    $el.append(data.container);
+    var $table = $el.find('table');
+    if (data.class) $table.addClass(data.class);
+    if (data.caption) $table.prepend(data.caption);
+
+    if (!data.selection) data.selection = {
+      mode: 'none', selected: null, target: 'row', selectable: null
+    };
+    if (HTMLWidgets.shinyMode && data.selection.mode !== 'none' &&
+        data.selection.target === 'row+column') {
+      if ($table.children('tfoot').length === 0) {
+        $table.append($(''));
+        $table.find('thead tr').clone().appendTo($table.find('tfoot'));
+      }
+    }
+
+    // column filters
+    var filterRow;
+    switch (data.filter) {
+      case 'top':
+        $table.children('thead').append(data.filterHTML);
+        filterRow = $table.find('thead tr:last td');
+        break;
+      case 'bottom':
+        if ($table.children('tfoot').length === 0) {
+          $table.append($(''));
+        }
+        $table.children('tfoot').prepend(data.filterHTML);
+        filterRow = $table.find('tfoot tr:first td');
+        break;
+    }
+
+    var options = { searchDelay: 1000 };
+    if (cells !== null) $.extend(options, {
+      data: cells
+    });
+
+    // options for fillContainer
+    var bootstrapActive = typeof($.fn.popover) != 'undefined';
+    if (instance.fillContainer) {
+
+      // force scrollX/scrollY and turn off autoWidth
+      options.scrollX = true;
+      options.scrollY = "100px"; // can be any value, we'll adjust below
+
+      // if we aren't paginating then move around the info/filter controls
+      // to save space at the bottom and rephrase the info callback
+      if (data.options.paging === false) {
+
+        // we know how to do this cleanly for bootstrap, not so much
+        // for other themes/layouts
+        if (bootstrapActive) {
+          options.dom = "<'row'<'col-sm-4'i><'col-sm-8'f>>" +
+                        "<'row'<'col-sm-12'tr>>";
+        }
+
+        options.fnInfoCallback = function(oSettings, iStart, iEnd,
+                                           iMax, iTotal, sPre) {
+          return Number(iTotal).toLocaleString() + " records";
+        };
+      }
+    }
+
+    // auto hide navigation if requested
+    // Note, this only works on client-side processing mode as on server-side,
+    // cells (data.data) is null; In addition, we require the pageLength option
+    // being provided explicitly to enable this. Despite we may be able to deduce
+    // the default value of pageLength, it may complicate things so we'd rather
+    // put this responsiblity to users and warn them on the R side.
+    if (data.autoHideNavigation === true && data.options.paging !== false) {
+      // strip all nav if length >= cells
+      if ((cells instanceof Array) && data.options.pageLength >= cells.length)
+        options.dom = bootstrapActive ? "<'row'<'col-sm-12'tr>>" : "t";
+      // alternatively lean things out for flexdashboard mobile portrait
+      else if (bootstrapActive && window.FlexDashboard && window.FlexDashboard.isMobilePhone())
+        options.dom = "<'row'<'col-sm-12'f>>" +
+                      "<'row'<'col-sm-12'tr>>"  +
+                      "<'row'<'col-sm-12'p>>";
+    }
+
+    $.extend(true, options, data.options || {});
+
+    var searchCols = options.searchCols;
+    if (searchCols) {
+      searchCols = searchCols.map(function(x) {
+        return x === null ? '' : x.search;
+      });
+      // FIXME: this means I don't respect the escapeRegex setting
+      delete options.searchCols;
+    }
+
+    // server-side processing?
+    var server = options.serverSide === true;
+
+    // use the dataSrc function to pre-process JSON data returned from R
+    var DT_rows_all = [], DT_rows_current = [];
+    if (server && HTMLWidgets.shinyMode && typeof options.ajax === 'object' &&
+        /^session\/[\da-z]+\/dataobj/.test(options.ajax.url) && !options.ajax.dataSrc) {
+      options.ajax.dataSrc = function(json) {
+        DT_rows_all = $.makeArray(json.DT_rows_all);
+        DT_rows_current = $.makeArray(json.DT_rows_current);
+        var data = json.data;
+        if (!colReorderEnabled()) return data;
+        var table = $table.DataTable(), order = table.colReorder.order(), flag = true, i, j, row;
+        for (i = 0; i < order.length; ++i) if (order[i] !== i) flag = false;
+        if (flag) return data;
+        for (i = 0; i < data.length; ++i) {
+          row = data[i].slice();
+          for (j = 0; j < order.length; ++j) data[i][j] = row[order[j]];
+        }
+        return data;
+      };
+    }
+
+    var thiz = this;
+    if (instance.fillContainer) $table.on('init.dt', function(e) {
+      thiz.fillAvailableHeight(el, $(el).innerHeight());
+    });
+    // If the page contains serveral datatables and one of which enables colReorder,
+    // the table.colReorder.order() function will exist but throws error when called.
+    // So it seems like the only way to know if colReorder is enabled or not is to
+    // check the options.
+    var colReorderEnabled = function() { return "colReorder" in options; };
+    var table = $table.DataTable(options);
+    $el.data('datatable', table);
+
+    // Unregister previous Crosstalk event subscriptions, if they exist
+    if (instance.ctfilterSubscription) {
+      instance.ctfilterHandle.off("change", instance.ctfilterSubscription);
+      instance.ctfilterSubscription = null;
+    }
+    if (instance.ctselectSubscription) {
+      instance.ctselectHandle.off("change", instance.ctselectSubscription);
+      instance.ctselectSubscription = null;
+    }
+
+    if (!crosstalkOptions.group) {
+      $table[0].ctfilter = null;
+      $table[0].ctselect = null;
+    } else {
+      var key = crosstalkOptions.key;
+      function keysToMatches(keys) {
+        if (!keys) {
+          return null;
+        } else {
+          var selectedKeys = {};
+          for (var i = 0; i < keys.length; i++) {
+            selectedKeys[keys[i]] = true;
+          }
+          var matches = {};
+          for (var j = 0; j < key.length; j++) {
+            if (selectedKeys[key[j]])
+              matches[j] = true;
+          }
+          return matches;
+        }
+      }
+
+      function applyCrosstalkFilter(e) {
+        $table[0].ctfilter = keysToMatches(e.value);
+        table.draw();
+      }
+      instance.ctfilterSubscription = instance.ctfilterHandle.on("change", applyCrosstalkFilter);
+      applyCrosstalkFilter({value: instance.ctfilterHandle.filteredKeys});
+
+      function applyCrosstalkSelection(e) {
+        if (e.sender !== instance.ctselectHandle) {
+          table
+            .rows('.' + selClass, {search: 'applied'})
+            .nodes()
+            .to$()
+            .removeClass(selClass);
+          if (selectedRows)
+            changeInput('rows_selected', selectedRows(), void 0, true);
+        }
+
+        if (e.sender !== instance.ctselectHandle && e.value && e.value.length) {
+          var matches = keysToMatches(e.value);
+
+          // persistent selection with plotly (& leaflet)
+          var ctOpts = crosstalk.var("plotlyCrosstalkOpts").get() || {};
+          if (ctOpts.persistent === true) {
+            var matches = $.extend(matches, $table[0].ctselect);
+          }
+
+          $table[0].ctselect = matches;
+          table.draw();
+        } else {
+          if ($table[0].ctselect) {
+            $table[0].ctselect = null;
+            table.draw();
+          }
+        }
+      }
+      instance.ctselectSubscription = instance.ctselectHandle.on("change", applyCrosstalkSelection);
+      // TODO: This next line doesn't seem to work when renderDataTable is used
+      applyCrosstalkSelection({value: instance.ctselectHandle.value});
+    }
+
+    var inArray = function(val, array) {
+      return $.inArray(val, $.makeArray(array)) > -1;
+    };
+
+    // search the i-th column
+    var searchColumn = function(i, value) {
+      var regex = false, ci = true;
+      if (options.search) {
+        regex = options.search.regex,
+        ci = options.search.caseInsensitive !== false;
+      }
+      // need to transpose the column index when colReorder is enabled
+      if (table.colReorder) i = table.colReorder.transpose(i);
+      return table.column(i).search(value, regex, !regex, ci);
+    };
+
+    if (data.filter !== 'none') {
+
+      filterRow.each(function(i, td) {
+
+        var $td = $(td), type = $td.data('type'), filter;
+        var $input = $td.children('div').first().children('input');
+        var disabled = $input.prop('disabled');
+        var searchable = table.settings()[0].aoColumns[i].bSearchable;
+        $input.prop('disabled', !searchable || disabled);
+        $input.data('searchable', searchable); // for updating later
+        $input.on('input blur', function() {
+          $input.next('span').toggle(Boolean($input.val()));
+        });
+        // Bootstrap sets pointer-events to none and we won't be able to click
+        // the clear button
+        $input.next('span').css('pointer-events', 'auto').hide().click(function() {
+          $(this).hide().prev('input').val('').trigger('input').focus();
+        });
+        var searchCol;  // search string for this column
+        if (searchCols && searchCols[i]) {
+          searchCol = searchCols[i];
+          $input.val(searchCol).trigger('input');
+        }
+        var $x = $td.children('div').last();
+
+        // remove the overflow: hidden attribute of the scrollHead
+        // (otherwise the scrolling table body obscures the filters)
+        // The workaround and the discussion from
+        // https://github.com/rstudio/DT/issues/554#issuecomment-518007347
+        // Otherwise the filter selection will not be anchored to the values
+        // when the columns number is many and scrollX is enabled.
+        var scrollHead = $(el).find('.dataTables_scrollHead,.dataTables_scrollFoot');
+        var cssOverflowHead = scrollHead.css('overflow');
+        var scrollBody = $(el).find('.dataTables_scrollBody');
+        var cssOverflowBody = scrollBody.css('overflow');
+        var scrollTable = $(el).find('.dataTables_scroll');
+        var cssOverflowTable = scrollTable.css('overflow');
+        if (cssOverflowHead === 'hidden') {
+          $x.on('show hide', function(e) {
+            if (e.type === 'show') {
+              scrollHead.css('overflow', 'visible');
+              scrollBody.css('overflow', 'visible');
+              scrollTable.css('overflow-x', 'scroll');
+            } else {
+              scrollHead.css('overflow', cssOverflowHead);
+              scrollBody.css('overflow', cssOverflowBody);
+              scrollTable.css('overflow-x', cssOverflowTable);
+            }
+          });
+          $x.css('z-index', 25);
+        }
+
+        if (inArray(type, ['factor', 'logical'])) {
+          $input.on({
+            click: function() {
+              $input.parent().hide(); $x.show().trigger('show'); filter[0].selectize.focus();
+            },
+            input: function() {
+              var v1 = JSON.stringify(filter[0].selectize.getValue()), v2 = $input.val();
+              if (v1 === '[]') v1 = '';
+              if (v1 !== v2) filter[0].selectize.setValue(v2 === '' ? [] : JSON.parse(v2));
+            }
+          });
+          var $input2 = $x.children('select');
+          filter = $input2.selectize({
+            options: $input2.data('options').map(function(v, i) {
+              return ({text: v, value: v});
+            }),
+            plugins: ['remove_button'],
+            hideSelected: true,
+            onChange: function(value) {
+              if (value === null) value = []; // compatibility with jQuery 3.0
+              $input.val(value.length ? JSON.stringify(value) : '');
+              if (value.length) $input.trigger('input');
+              $input.attr('title', $input.val());
+              if (server) {
+                searchColumn(i, value.length ? JSON.stringify(value) : '').draw();
+                return;
+              }
+              // turn off filter if nothing selected
+              $td.data('filter', value.length > 0);
+              table.draw();  // redraw table, and filters will be applied
+            }
+          });
+          if (searchCol) filter[0].selectize.setValue(JSON.parse(searchCol));
+          filter[0].selectize.on('blur', function() {
+            $x.hide().trigger('hide'); $input.parent().show(); $input.trigger('blur');
+          });
+          filter.next('div').css('margin-bottom', 'auto');
+        } else if (type === 'character') {
+          var fun = function() {
+            searchColumn(i, $input.val()).draw();
+          };
+          if (server) {
+            fun = $.fn.dataTable.util.throttle(fun, options.searchDelay);
+          }
+          $input.on('input', fun);
+        } else if (inArray(type, ['number', 'integer', 'date', 'time'])) {
+          var $x0 = $x;
+          $x = $x0.children('div').first();
+          $x0.css({
+            'background-color': '#fff',
+            'border': '1px #ddd solid',
+            'border-radius': '4px',
+            'padding': data.vertical ? '35px 20px': '20px 20px 10px 20px'
+          });
+          var $spans = $x0.children('span').css({
+            'margin-top': data.vertical ? '0' : '10px',
+            'white-space': 'nowrap'
+          });
+          var $span1 = $spans.first(), $span2 = $spans.last();
+          var r1 = +$x.data('min'), r2 = +$x.data('max');
+          // when the numbers are too small or have many decimal places, the
+          // slider may have numeric precision problems (#150)
+          var scale = Math.pow(10, Math.max(0, +$x.data('scale') || 0));
+          r1 = Math.round(r1 * scale); r2 = Math.round(r2 * scale);
+          var scaleBack = function(x, scale) {
+            if (scale === 1) return x;
+            var d = Math.round(Math.log(scale) / Math.log(10));
+            // to avoid problems like 3.423/100 -> 0.034230000000000003
+            return (x / scale).toFixed(d);
+          };
+          var slider_min = function() {
+            return filter.noUiSlider('options').range.min;
+          };
+          var slider_max = function() {
+            return filter.noUiSlider('options').range.max;
+          };
+          $input.on({
+            focus: function() {
+              $x0.show().trigger('show');
+              // first, make sure the slider div leaves at least 20px between
+              // the two (slider value) span's
+              $x0.width(Math.max(160, $span1.outerWidth() + $span2.outerWidth() + 20));
+              // then, if the input is really wide or slider is vertical,
+              // make the slider the same width as the input
+              if ($x0.outerWidth() < $input.outerWidth() || data.vertical) {
+                $x0.outerWidth($input.outerWidth());
+              }
+              // make sure the slider div does not reach beyond the right margin
+              if ($(window).width() < $x0.offset().left + $x0.width()) {
+                $x0.offset({
+                  'left': $input.offset().left + $input.outerWidth() - $x0.outerWidth()
+                });
+              }
+            },
+            blur: function() {
+              $x0.hide().trigger('hide');
+            },
+            input: function() {
+              if ($input.val() === '') filter.val([slider_min(), slider_max()]);
+            },
+            change: function() {
+              var v = $input.val().replace(/\s/g, '');
+              if (v === '') return;
+              v = v.split('...');
+              if (v.length !== 2) {
+                $input.parent().addClass('has-error');
+                return;
+              }
+              if (v[0] === '') v[0] = slider_min();
+              if (v[1] === '') v[1] = slider_max();
+              $input.parent().removeClass('has-error');
+              // treat date as UTC time at midnight
+              var strTime = function(x) {
+                var s = type === 'date' ? 'T00:00:00Z' : '';
+                var t = new Date(x + s).getTime();
+                // add 10 minutes to date since it does not hurt the date, and
+                // it helps avoid the tricky floating point arithmetic problems,
+                // e.g. sometimes the date may be a few milliseconds earlier
+                // than the midnight due to precision problems in noUiSlider
+                return type === 'date' ? t + 3600000 : t;
+              };
+              if (inArray(type, ['date', 'time'])) {
+                v[0] = strTime(v[0]);
+                v[1] = strTime(v[1]);
+              }
+              if (v[0] != slider_min()) v[0] *= scale;
+              if (v[1] != slider_max()) v[1] *= scale;
+              filter.val(v);
+            }
+          });
+          var formatDate = function(d, isoFmt) {
+            d = scaleBack(d, scale);
+            if (type === 'number') return d;
+            if (type === 'integer') return parseInt(d);
+            var x = new Date(+d);
+            var fmt = ('filterDateFmt' in data) ? data.filterDateFmt[i] : undefined;
+            if (fmt !== undefined && isoFmt === false) return x[fmt.method].apply(x, fmt.params);
+            if (type === 'date') {
+              var pad0 = function(x) {
+                return ('0' + x).substr(-2, 2);
+              };
+              return x.getUTCFullYear() + '-' + pad0(1 + x.getUTCMonth())
+                      + '-' + pad0(x.getUTCDate());
+            } else {
+              return x.toISOString();
+            }
+          };
+          var opts = type === 'date' ? { step: 60 * 60 * 1000 } :
+                     type === 'integer' ? { step: 1 } : {};
+
+          opts.orientation = data.vertical ? 'vertical': 'horizontal';
+          opts.direction = data.vertical ? 'rtl': 'ltr';
+
+          filter = $x.noUiSlider($.extend({
+            start: [r1, r2],
+            range: {min: r1, max: r2},
+            connect: true
+          }, opts));
+          if (scale > 1) (function() {
+            var t1 = r1, t2 = r2;
+            var val = filter.val();
+            while (val[0] > r1 || val[1] < r2) {
+              if (val[0] > r1) {
+                t1 -= val[0] - r1;
+              }
+              if (val[1] < r2) {
+                t2 += r2 - val[1];
+              }
+              filter = $x.noUiSlider($.extend({
+                start: [t1, t2],
+                range: {min: t1, max: t2},
+                connect: true
+              }, opts), true);
+              val = filter.val();
+            }
+            r1  = t1; r2 = t2;
+          })();
+          var updateSliderText = function(v1, v2) {
+            $span1.text(formatDate(v1, false)); $span2.text(formatDate(v2, false));
+          };
+          updateSliderText(r1, r2);
+          var updateSlider = function(e) {
+            var val = filter.val();
+            // turn off filter if in full range
+            $td.data('filter', val[0] > slider_min() || val[1] < slider_max());
+            var v1 = formatDate(val[0]), v2 = formatDate(val[1]), ival;
+            if ($td.data('filter')) {
+              ival = v1 + ' ... ' + v2;
+              $input.attr('title', ival).val(ival).trigger('input');
+            } else {
+              $input.attr('title', '').val('');
+            }
+            updateSliderText(val[0], val[1]);
+            if (e.type === 'slide') return;  // no searching when sliding only
+            if (server) {
+              searchColumn(i, $td.data('filter') ? ival : '').draw();
+              return;
+            }
+            table.draw();
+          };
+          filter.on({
+            set: updateSlider,
+            slide: updateSlider
+          });
+        }
+
+        // server-side processing will be handled by R (or whatever server
+        // language you use); the following code is only needed for client-side
+        // processing
+        if (server) {
+          // if a search string has been pre-set, search now
+          if (searchCol) searchColumn(i, searchCol).draw();
+          return;
+        }
+
+        var customFilter = function(settings, data, dataIndex) {
+          // there is no way to attach a search function to a specific table,
+          // and we need to make sure a global search function is not applied to
+          // all tables (i.e. a range filter in a previous table should not be
+          // applied to the current table); we use the settings object to
+          // determine if we want to perform searching on the current table,
+          // since settings.sTableId will be different to different tables
+          if (table.settings()[0] !== settings) return true;
+          // no filter on this column or no need to filter this column
+          if (typeof filter === 'undefined' || !$td.data('filter')) return true;
+
+          var r = filter.val(), v, r0, r1;
+          var i_data = function(i) {
+            if (!colReorderEnabled()) return i;
+            var order = table.colReorder.order(), k;
+            for (k = 0; k < order.length; ++k) if (order[k] === i) return k;
+            return i; // in theory it will never be here...
+          }
+          v = data[i_data(i)];
+          if (type === 'number' || type === 'integer') {
+            v = parseFloat(v);
+            // how to handle NaN? currently exclude these rows
+            if (isNaN(v)) return(false);
+            r0 = parseFloat(scaleBack(r[0], scale))
+            r1 = parseFloat(scaleBack(r[1], scale));
+            if (v >= r0 && v <= r1) return true;
+          } else if (type === 'date' || type === 'time') {
+            v = new Date(v);
+            r0 = new Date(r[0] / scale); r1 = new Date(r[1] / scale);
+            if (v >= r0 && v <= r1) return true;
+          } else if (type === 'factor') {
+            if (r.length === 0 || inArray(v, r)) return true;
+          } else if (type === 'logical') {
+            if (r.length === 0) return true;
+            if (inArray(v === '' ? 'na' : v, r)) return true;
+          }
+          return false;
+        };
+
+        $.fn.dataTable.ext.search.push(customFilter);
+
+        // search for the preset search strings if it is non-empty
+        if (searchCol) {
+          if (inArray(type, ['factor', 'logical'])) {
+            filter[0].selectize.setValue(JSON.parse(searchCol));
+          } else if (type === 'character') {
+            $input.trigger('input');
+          } else if (inArray(type, ['number', 'integer', 'date', 'time'])) {
+            $input.trigger('change');
+          }
+        }
+
+      });
+
+    }
+
+    // highlight search keywords
+    var highlight = function() {
+      var body = $(table.table().body());
+      // removing the old highlighting first
+      body.unhighlight();
+
+      // don't highlight the "not found" row, so we get the rows using the api
+      if (table.rows({ filter: 'applied' }).data().length === 0) return;
+      // highlight global search keywords
+      body.highlight($.trim(table.search()).split(/\s+/));
+      // then highlight keywords from individual column filters
+      if (filterRow) filterRow.each(function(i, td) {
+        var $td = $(td), type = $td.data('type');
+        if (type !== 'character') return;
+        var $input = $td.children('div').first().children('input');
+        var column = table.column(i).nodes().to$(),
+            val = $.trim($input.val());
+        if (type !== 'character' || val === '') return;
+        column.highlight(val.split(/\s+/));
+      });
+    };
+
+    if (options.searchHighlight) {
+      table
+      .on('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth', highlight)
+      .on('destroy', function() {
+        // remove event handler
+        table.off('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth');
+      });
+
+      // Set the option for escaping regex characters in our search string.  This will be used
+      // for all future matching.
+      jQuery.fn.highlight.options.escapeRegex = (!options.search || !options.search.regex);
+
+      // initial highlight for state saved conditions and initial states
+      highlight();
+    }
+
+    // run the callback function on the table instance
+    if (typeof data.callback === 'function') data.callback(table);
+
+    // double click to edit the cell, row, column, or all cells
+    if (data.editable) table.on('dblclick.dt', 'tbody td', function(e) {
+      // only bring up the editor when the cell itself is dbclicked, and ignore
+      // other dbclick events bubbled up (e.g. from the )
+      if (e.target !== this) return;
+      var target = [], immediate = false;
+      switch (data.editable.target) {
+        case 'cell':
+          target = [this];
+          immediate = true;  // edit will take effect immediately
+          break;
+        case 'row':
+          target = table.cells(table.cell(this).index().row, '*').nodes();
+          break;
+        case 'column':
+          target = table.cells('*', table.cell(this).index().column).nodes();
+          break;
+        case 'all':
+          target = table.cells().nodes();
+          break;
+        default:
+          throw 'The editable parameter must be "cell", "row", "column", or "all"';
+      }
+      var disableCols = data.editable.disable ? data.editable.disable.columns : null;
+      var numericCols = data.editable.numeric;
+      var areaCols = data.editable.area;
+      var dateCols = data.editable.date;
+      for (var i = 0; i < target.length; i++) {
+        (function(cell, current) {
+          var $cell = $(cell), html = $cell.html();
+          var _cell = table.cell(cell), value = _cell.data(), index = _cell.index().column;
+          var $input;
+          if (inArray(index, numericCols)) {
+            $input = $('');
+          } else if (inArray(index, areaCols)) {
+            $input = $('');
+          } else if (inArray(index, dateCols)) {
+            $input = $('');
+          } else {
+            $input = $('');
+          }
+          if (!immediate) {
+            $cell.data('input', $input).data('html', html);
+            $input.attr('title', 'Hit Ctrl+Enter to finish editing, or Esc to cancel');
+          }
+          $input.val(value);
+          if (inArray(index, disableCols)) {
+            $input.attr('readonly', '').css('filter', 'invert(25%)');
+          }
+          $cell.empty().append($input);
+          if (cell === current) $input.focus();
+          $input.css('width', '100%');
+
+          if (immediate) $input.on('blur', function(e) {
+            var valueNew = $input.val();
+            if (valueNew !== value) {
+              _cell.data(valueNew);
+              if (HTMLWidgets.shinyMode) {
+                changeInput('cell_edit', [cellInfo(cell)], 'DT.cellInfo', null, {priority: 'event'});
+              }
+              // for server-side processing, users have to call replaceData() to update the table
+              if (!server) table.draw(false);
+            } else {
+              $cell.html(html);
+            }
+          }).on('keyup', function(e) {
+            // hit Escape to cancel editing
+            if (e.keyCode === 27) $input.trigger('blur');
+          });
+
+          // bulk edit (row, column, or all)
+          if (!immediate) $input.on('keyup', function(e) {
+            var removeInput = function($cell, restore) {
+              $cell.data('input').remove();
+              if (restore) $cell.html($cell.data('html'));
+            }
+            if (e.keyCode === 27) {
+              for (var i = 0; i < target.length; i++) {
+                removeInput($(target[i]), true);
+              }
+            } else if (e.keyCode === 13 && e.ctrlKey) {
+              // Ctrl + Enter
+              var cell, $cell, _cell, cellData = [];
+              for (var i = 0; i < target.length; i++) {
+                cell = target[i]; $cell = $(cell); _cell = table.cell(cell);
+                _cell.data($cell.data('input').val());
+                HTMLWidgets.shinyMode && cellData.push(cellInfo(cell));
+                removeInput($cell, false);
+              }
+              if (HTMLWidgets.shinyMode) {
+                changeInput('cell_edit', cellData, 'DT.cellInfo', null, {priority: "event"});
+              }
+              if (!server) table.draw(false);
+            }
+          });
+        })(target[i], this);
+      }
+    });
+
+    // interaction with shiny
+    if (!HTMLWidgets.shinyMode && !crosstalkOptions.group) return;
+
+    var methods = {};
+    var shinyData = {};
+
+    methods.updateCaption = function(caption) {
+      if (!caption) return;
+      $table.children('caption').replaceWith(caption);
+    }
+
+    // register clear functions to remove input values when the table is removed
+    instance.clearInputs = {};
+
+    var changeInput = function(id, value, type, noCrosstalk, opts) {
+      var event = id;
+      id = el.id + '_' + id;
+      if (type) id = id + ':' + type;
+      // do not update if the new value is the same as old value
+      if (event !== 'cell_edit' && !/_clicked$/.test(event) && shinyData.hasOwnProperty(id) && shinyData[id] === JSON.stringify(value))
+        return;
+      shinyData[id] = JSON.stringify(value);
+      if (HTMLWidgets.shinyMode && Shiny.setInputValue) {
+        Shiny.setInputValue(id, value, opts);
+        if (!instance.clearInputs[id]) instance.clearInputs[id] = function() {
+          Shiny.setInputValue(id, null);
+        }
+      }
+
+      // HACK
+      if (event === "rows_selected" && !noCrosstalk) {
+        if (crosstalkOptions.group) {
+          var keys = crosstalkOptions.key;
+          var selectedKeys = null;
+          if (value) {
+            selectedKeys = [];
+            for (var i = 0; i < value.length; i++) {
+              // The value array's contents use 1-based row numbers, so we must
+              // convert to 0-based before indexing into the keys array.
+              selectedKeys.push(keys[value[i] - 1]);
+            }
+          }
+          instance.ctselectHandle.set(selectedKeys);
+        }
+      }
+    };
+
+    var addOne = function(x) {
+      return x.map(function(i) { return 1 + i; });
+    };
+
+    var unique = function(x) {
+      var ux = [];
+      $.each(x, function(i, el){
+        if ($.inArray(el, ux) === -1) ux.push(el);
+      });
+      return ux;
+    }
+
+    // change the row index of a cell
+    var tweakCellIndex = function(cell) {
+      var info = cell.index();
+      // some cell may not be valid. e.g, #759
+      // when using the RowGroup extension, datatables will
+      // generate the row label and the cells are not part of
+      // the data thus contain no row/col info
+      if (info === undefined)
+        return {row: null, col: null};
+      if (server) {
+        info.row = DT_rows_current[info.row];
+      } else {
+        info.row += 1;
+      }
+      return {row: info.row, col: info.column};
+    }
+
+    var cleanSelectedValues = function() {
+      changeInput('rows_selected', []);
+      changeInput('columns_selected', []);
+      changeInput('cells_selected', transposeArray2D([]), 'shiny.matrix');
+    }
+    // #828 we should clean the selection on the server-side when the table reloads
+    cleanSelectedValues();
+
+    // a flag to indicates if select extension is initialized or not
+    var flagSelectExt = table.settings()[0]._select !== undefined;
+    // the Select extension should only be used in the client mode and
+    // when the selection.mode is set to none
+    if (data.selection.mode === 'none' && !server && flagSelectExt) {
+      var updateRowsSelected = function() {
+        var rows = table.rows({selected: true});
+        var selected = [];
+        $.each(rows.indexes().toArray(), function(i, v) {
+          selected.push(v + 1);
+        });
+        changeInput('rows_selected', selected);
+      }
+      var updateColsSelected = function() {
+        var columns = table.columns({selected: true});
+        changeInput('columns_selected', columns.indexes().toArray());
+      }
+      var updateCellsSelected = function() {
+        var cells = table.cells({selected: true});
+        var selected = [];
+        cells.every(function() {
+          var row = this.index().row;
+          var col = this.index().column;
+          selected = selected.concat([[row + 1, col]]);
+        });
+        changeInput('cells_selected', transposeArray2D(selected), 'shiny.matrix');
+      }
+      table.on('select deselect', function(e, dt, type, indexes) {
+        updateRowsSelected();
+        updateColsSelected();
+        updateCellsSelected();
+      })
+    }
+
+    var selMode = data.selection.mode, selTarget = data.selection.target;
+    var selDisable = data.selection.selectable === false;
+    if (inArray(selMode, ['single', 'multiple'])) {
+      var selClass = inArray(data.style, ['bootstrap', 'bootstrap4']) ? 'active' : 'selected';
+      // selected1: row indices; selected2: column indices
+      var initSel = function(x) {
+        if (x === null || typeof x === 'boolean' || selTarget === 'cell') {
+          return {rows: [], cols: []};
+        } else if (selTarget === 'row') {
+          return {rows: $.makeArray(x), cols: []};
+        } else if (selTarget === 'column') {
+          return {rows: [], cols: $.makeArray(x)};
+        } else if (selTarget === 'row+column') {
+          return {rows: $.makeArray(x.rows), cols: $.makeArray(x.cols)};
+        }
+      }
+      var selected = data.selection.selected;
+      var selected1 = initSel(selected).rows, selected2 = initSel(selected).cols;
+      // selectable should contain either all positive or all non-positive values, not both
+      // positive values indicate "selectable" while non-positive values means "nonselectable"
+      // the assertion is performed on R side. (only column indicides could be zero which indicates
+      // the row name)
+      var selectable = data.selection.selectable;
+      var selectable1 = initSel(selectable).rows, selectable2 = initSel(selectable).cols;
+
+      // After users reorder the rows or filter the table, we cannot use the table index
+      // directly. Instead, we need this function to find out the rows between the two clicks.
+      // If user filter the table again between the start click and the end click, the behavior
+      // would be undefined, but it should not be a problem.
+      var shiftSelRowsIndex = function(start, end) {
+        var indexes = server ? DT_rows_all : table.rows({ search: 'applied' }).indexes().toArray();
+        start = indexes.indexOf(start); end = indexes.indexOf(end);
+        // if start is larger than end, we need to swap
+        if (start > end) {
+          var tmp = end; end = start; start = tmp;
+        }
+        return indexes.slice(start, end + 1);
+      }
+
+      var serverRowIndex = function(clientRowIndex) {
+        return server ? DT_rows_current[clientRowIndex] : clientRowIndex + 1;
+      }
+
+      // row, column, or cell selection
+      var lastClickedRow;
+      if (inArray(selTarget, ['row', 'row+column'])) {
+        // Get the current selected rows. It will also
+        // update the selected1's value based on the current row selection state
+        // Note we can't put this function inside selectRows() directly,
+        // the reason is method.selectRows() will override selected1's value but this
+        // function will add rows to selected1 (keep the existing selection), which is
+        // inconsistent with column and cell selection.
+        var selectedRows = function() {
+          var rows = table.rows('.' + selClass);
+          var idx = rows.indexes().toArray();
+          if (!server) {
+            selected1 = addOne(idx);
+            return selected1;
+          }
+          idx = idx.map(function(i) {
+            return DT_rows_current[i];
+          });
+          selected1 = selMode === 'multiple' ? unique(selected1.concat(idx)) : idx;
+          return selected1;
+        }
+        // Change selected1's value based on selectable1, then refresh the row state
+        var onlyKeepSelectableRows = function() {
+          if (selDisable) { // users can't select; useful when only want backend select
+            selected1 = [];
+            return;
+          }
+          if (selectable1.length === 0) return;
+          var nonselectable = selectable1[0] <= 0;
+          if (nonselectable) {
+            // should make selectable1 positive
+            selected1 = $(selected1).not(selectable1.map(function(i) { return -i; })).get();
+          } else {
+            selected1 = $(selected1).filter(selectable1).get();
+          }
+        }
+        // Change selected1's value based on selectable1, then
+        // refresh the row selection state according to values in selected1
+        var selectRows = function(ignoreSelectable) {
+          if (!ignoreSelectable) onlyKeepSelectableRows();
+          table.$('tr.' + selClass).removeClass(selClass);
+          if (selected1.length === 0) return;
+          if (server) {
+            table.rows({page: 'current'}).every(function() {
+              if (inArray(DT_rows_current[this.index()], selected1)) {
+                $(this.node()).addClass(selClass);
+              }
+            });
+          } else {
+            var selected0 = selected1.map(function(i) { return i - 1; });
+            $(table.rows(selected0).nodes()).addClass(selClass);
+          }
+        }
+        table.on('mousedown.dt', 'tbody tr', function(e) {
+          var $this = $(this), thisRow = table.row(this);
+          if (selMode === 'multiple') {
+            if (e.shiftKey && lastClickedRow !== undefined) {
+              // select or de-select depends on the last clicked row's status
+              var flagSel = !$this.hasClass(selClass);
+              var crtClickedRow = serverRowIndex(thisRow.index());
+              if (server) {
+                var rowsIndex = shiftSelRowsIndex(lastClickedRow, crtClickedRow);
+                // update current page's selClass
+                rowsIndex.map(function(i) {
+                  var rowIndex = DT_rows_current.indexOf(i);
+                  if (rowIndex >= 0) {
+                    var row = table.row(rowIndex).nodes().to$();
+                    var flagRowSel = !row.hasClass(selClass);
+                    if (flagSel === flagRowSel) row.toggleClass(selClass);
+                  }
+                });
+                // update selected1
+                if (flagSel) {
+                  selected1 = unique(selected1.concat(rowsIndex));
+                } else {
+                  selected1 = selected1.filter(function(index) {
+                    return !inArray(index, rowsIndex);
+                  });
+                }
+              } else {
+                // js starts from 0
+                shiftSelRowsIndex(lastClickedRow - 1, crtClickedRow - 1).map(function(value) {
+                  var row = table.row(value).nodes().to$();
+                  var flagRowSel = !row.hasClass(selClass);
+                  if (flagSel === flagRowSel) row.toggleClass(selClass);
+                });
+              }
+              e.preventDefault();
+            } else {
+              $this.toggleClass(selClass);
+            }
+          } else {
+            if ($this.hasClass(selClass)) {
+              $this.removeClass(selClass);
+            } else {
+              table.$('tr.' + selClass).removeClass(selClass);
+              $this.addClass(selClass);
+            }
+          }
+          if (server && !$this.hasClass(selClass)) {
+            var id = DT_rows_current[thisRow.index()];
+            // remove id from selected1 since its class .selected has been removed
+            if (inArray(id, selected1)) selected1.splice($.inArray(id, selected1), 1);
+          }
+          selectedRows(); // update selected1's value based on selClass
+          selectRows(false); // only keep the selectable rows
+          changeInput('rows_selected', selected1);
+          changeInput('row_last_clicked', serverRowIndex(thisRow.index()), null, null, {priority: 'event'});
+          lastClickedRow = serverRowIndex(thisRow.index());
+        });
+        selectRows(false);  // in case users have specified pre-selected rows
+        // restore selected rows after the table is redrawn (e.g. sort/search/page);
+        // client-side tables will preserve the selections automatically; for
+        // server-side tables, we have to *real* row indices are in `selected1`
+        changeInput('rows_selected', selected1);
+        if (server) table.on('draw.dt', function(e) { selectRows(false); });
+        methods.selectRows = function(selected, ignoreSelectable) {
+          selected1 = $.makeArray(selected);
+          selectRows(ignoreSelectable);
+          changeInput('rows_selected', selected1);
+        }
+      }
+
+      if (inArray(selTarget, ['column', 'row+column'])) {
+        if (selTarget === 'row+column') {
+          $(table.columns().footer()).css('cursor', 'pointer');
+        }
+        // update selected2's value based on selectable2
+        var onlyKeepSelectableCols = function() {
+          if (selDisable) { // users can't select; useful when only want backend select
+            selected2 = [];
+            return;
+          }
+          if (selectable2.length === 0) return;
+          var nonselectable = selectable2[0] <= 0;
+          if (nonselectable) {
+            // need to make selectable2 positive
+            selected2 = $(selected2).not(selectable2.map(function(i) { return -i; })).get();
+          } else {
+            selected2 = $(selected2).filter(selectable2).get();
+          }
+        }
+        // update selected2 and then
+        // refresh the col selection state according to values in selected2
+        var selectCols = function(ignoreSelectable) {
+          if (!ignoreSelectable) onlyKeepSelectableCols();
+          // if selected2 is not a valide index (e.g., larger than the column number)
+          // table.columns(selected2) will fail and result in a blank table
+          // this is different from the table.rows(), where the out-of-range indexes
+          // doesn't affect at all
+          selected2 = $(selected2).filter(table.columns().indexes()).get();
+          table.columns().nodes().flatten().to$().removeClass(selClass);
+          if (selected2.length > 0)
+            table.columns(selected2).nodes().flatten().to$().addClass(selClass);
+        }
+        var callback = function() {
+          var colIdx = selTarget === 'column' ? table.cell(this).index().column :
+              $.inArray(this, table.columns().footer()),
+              thisCol = $(table.column(colIdx).nodes());
+          if (colIdx === -1) return;
+          if (thisCol.hasClass(selClass)) {
+            thisCol.removeClass(selClass);
+            selected2.splice($.inArray(colIdx, selected2), 1);
+          } else {
+            if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass);
+            thisCol.addClass(selClass);
+            selected2 = selMode === 'single' ? [colIdx] : unique(selected2.concat([colIdx]));
+          }
+          selectCols(false); // update selected2 based on selectable
+          changeInput('columns_selected', selected2);
+        }
+        if (selTarget === 'column') {
+          $(table.table().body()).on('click.dt', 'td', callback);
+        } else {
+          $(table.table().footer()).on('click.dt', 'tr th', callback);
+        }
+        selectCols(false);  // in case users have specified pre-selected columns
+        changeInput('columns_selected', selected2);
+        if (server) table.on('draw.dt', function(e) { selectCols(false); });
+        methods.selectColumns = function(selected, ignoreSelectable) {
+          selected2 = $.makeArray(selected);
+          selectCols(ignoreSelectable);
+          changeInput('columns_selected', selected2);
+        }
+      }
+
+      if (selTarget === 'cell') {
+        var selected3 = [], selectable3 = [];
+        if (selected !== null) selected3 = selected;
+        if (selectable !== null && typeof selectable !== 'boolean') selectable3 = selectable;
+        var findIndex = function(ij, sel) {
+          for (var i = 0; i < sel.length; i++) {
+            if (ij[0] === sel[i][0] && ij[1] === sel[i][1]) return i;
+          }
+          return -1;
+        }
+         // Change selected3's value based on selectable3, then refresh the cell state
+        var onlyKeepSelectableCells = function() {
+          if (selDisable) { // users can't select; useful when only want backend select
+            selected3 = [];
+            return;
+          }
+          if (selectable3.length === 0) return;
+          var nonselectable = selectable3[0][0] <= 0;
+          var out = [];
+          if (nonselectable) {
+            selected3.map(function(ij) {
+              // should make selectable3 positive
+              if (findIndex([-ij[0], -ij[1]], selectable3) === -1) { out.push(ij); }
+            });
+          } else {
+            selected3.map(function(ij) {
+              if (findIndex(ij, selectable3) > -1) { out.push(ij); }
+            });
+          }
+          selected3 = out;
+        }
+        // Change selected3's value based on selectable3, then
+        // refresh the cell selection state according to values in selected3
+        var selectCells = function(ignoreSelectable) {
+          if (!ignoreSelectable) onlyKeepSelectableCells();
+          table.$('td.' + selClass).removeClass(selClass);
+          if (selected3.length === 0) return;
+          if (server) {
+            table.cells({page: 'current'}).every(function() {
+              var info = tweakCellIndex(this);
+              if (findIndex([info.row, info.col], selected3) > -1)
+                $(this.node()).addClass(selClass);
+            });
+          } else {
+            selected3.map(function(ij) {
+              $(table.cell(ij[0] - 1, ij[1]).node()).addClass(selClass);
+            });
+          }
+        };
+        table.on('click.dt', 'tbody td', function() {
+          var $this = $(this), info = tweakCellIndex(table.cell(this));
+          if ($this.hasClass(selClass)) {
+            $this.removeClass(selClass);
+            selected3.splice(findIndex([info.row, info.col], selected3), 1);
+          } else {
+            if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass);
+            $this.addClass(selClass);
+            selected3 = selMode === 'single' ? [[info.row, info.col]] :
+              unique(selected3.concat([[info.row, info.col]]));
+          }
+          selectCells(false); // must call this to update selected3 based on selectable3
+          changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix');
+        });
+        selectCells(false);  // in case users have specified pre-selected columns
+        changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix');
+
+        if (server) table.on('draw.dt', function(e) { selectCells(false); });
+        methods.selectCells = function(selected, ignoreSelectable) {
+          selected3 = selected ? selected : [];
+          selectCells(ignoreSelectable);
+          changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix');
+        }
+      }
+    }
+
+    // expose some table info to Shiny
+    var updateTableInfo = function(e, settings) {
+      // TODO: is anyone interested in the page info?
+      // changeInput('page_info', table.page.info());
+      var updateRowInfo = function(id, modifier) {
+        var idx;
+        if (server) {
+          idx = modifier.page === 'current' ? DT_rows_current : DT_rows_all;
+        } else {
+          var rows = table.rows($.extend({
+            search: 'applied',
+            page: 'all'
+          }, modifier));
+          idx = addOne(rows.indexes().toArray());
+        }
+        changeInput('rows' + '_' + id, idx);
+      };
+      updateRowInfo('current', {page: 'current'});
+      updateRowInfo('all', {});
+    }
+    table.on('draw.dt', updateTableInfo);
+    updateTableInfo();
+
+    // state info
+    table.on('draw.dt column-visibility.dt', function() {
+      changeInput('state', table.state());
+    });
+    changeInput('state', table.state());
+
+    // search info
+    var updateSearchInfo = function() {
+      changeInput('search', table.search());
+      if (filterRow) changeInput('search_columns', filterRow.toArray().map(function(td) {
+        return $(td).find('input').first().val();
+      }));
+    }
+    table.on('draw.dt', updateSearchInfo);
+    updateSearchInfo();
+
+    var cellInfo = function(thiz) {
+      var info = tweakCellIndex(table.cell(thiz));
+      info.value = table.cell(thiz).data();
+      return info;
+    }
+    // the current cell clicked on
+    table.on('click.dt', 'tbody td', function() {
+      changeInput('cell_clicked', cellInfo(this), null, null, {priority: 'event'});
+    })
+    changeInput('cell_clicked', {});
+
+    // do not trigger table selection when clicking on links unless they have classes
+    table.on('mousedown.dt', 'tbody td a', function(e) {
+      if (this.className === '') e.stopPropagation();
+    });
+
+    methods.addRow = function(data, rowname, resetPaging) {
+      var n = table.columns().indexes().length, d = n - data.length;
+      if (d === 1) {
+        data = rowname.concat(data)
+      } else if (d !== 0) {
+        console.log(data);
+        console.log(table.columns().indexes());
+        throw 'New data must be of the same length as current data (' + n + ')';
+      };
+      table.row.add(data).draw(resetPaging);
+    }
+
+    methods.updateSearch = function(keywords) {
+      if (keywords.global !== null)
+        $(table.table().container()).find('input[type=search]').first()
+             .val(keywords.global).trigger('input');
+      var columns = keywords.columns;
+      if (!filterRow || columns === null) return;
+      filterRow.toArray().map(function(td, i) {
+        var v = typeof columns === 'string' ? columns : columns[i];
+        if (typeof v === 'undefined') {
+          console.log('The search keyword for column ' + i + ' is undefined')
+          return;
+        }
+        $(td).find('input').first().val(v).trigger('input');
+        searchColumn(i, v);
+      });
+      table.draw();
+    }
+
+    methods.hideCols = function(hide, reset) {
+      if (reset) table.columns().visible(true, false);
+      table.columns(hide).visible(false);
+    }
+
+    methods.showCols = function(show, reset) {
+      if (reset) table.columns().visible(false, false);
+      table.columns(show).visible(true);
+    }
+
+    methods.colReorder = function(order, origOrder) {
+      table.colReorder.order(order, origOrder);
+    }
+
+    methods.selectPage = function(page) {
+      if (table.page.info().pages < page || page < 1) {
+        throw 'Selected page is out of range';
+      };
+      table.page(page - 1).draw(false);
+    }
+
+    methods.reloadData = function(resetPaging, clearSelection) {
+      // empty selections first if necessary
+      if (methods.selectRows && inArray('row', clearSelection)) methods.selectRows([]);
+      if (methods.selectColumns && inArray('column', clearSelection)) methods.selectColumns([]);
+      if (methods.selectCells && inArray('cell', clearSelection)) methods.selectCells([]);
+      table.ajax.reload(null, resetPaging);
+    }
+
+    // update table filters (set new limits of sliders)
+    methods.updateFilters = function(newProps) {
+      // loop through each filter in the filter row
+      filterRow.each(function(i, td) {
+        var k = i;
+        if (filterRow.length > newProps.length) {
+          if (i === 0) return;  // first column is row names
+          k = i - 1;
+        }
+        // Update the filters to reflect the updated data.
+        // Allow "falsy" (e.g. NULL) to signify a no-op.
+        if (newProps[k]) {
+          setFilterProps(td, newProps[k]);
+        }
+      });
+    };
+
+    table.shinyMethods = methods;
+  },
+  resize: function(el, width, height, instance) {
+    if (instance.data) this.renderValue(el, instance.data, instance);
+
+    // dynamically adjust height if fillContainer = TRUE
+    if (instance.fillContainer)
+      this.fillAvailableHeight(el, height);
+
+    this.adjustWidth(el);
+  },
+
+  // dynamically set the scroll body to fill available height
+  // (used with fillContainer = TRUE)
+  fillAvailableHeight: function(el, availableHeight) {
+
+    // see how much of the table is occupied by header/footer elements
+    // and use that to compute a target scroll body height
+    var dtWrapper = $(el).find('div.dataTables_wrapper');
+    var dtScrollBody = $(el).find($('div.dataTables_scrollBody'));
+    var framingHeight = dtWrapper.innerHeight() - dtScrollBody.innerHeight();
+    var scrollBodyHeight = availableHeight - framingHeight;
+
+    // we need to set `max-height` to none as datatables library now sets this
+    // to a fixed height, disabling the ability to resize to fill the window,
+    // as it will be set to a fixed 100px under such circumstances, e.g., RStudio IDE,
+    // or FlexDashboard
+    // see https://github.com/rstudio/DT/issues/951#issuecomment-1026464509
+    dtScrollBody.css('max-height', 'none');
+    // set the height
+    dtScrollBody.height(scrollBodyHeight + 'px');
+  },
+
+  // adjust the width of columns; remove the hard-coded widths on table and the
+  // scroll header when scrollX/Y are enabled
+  adjustWidth: function(el) {
+    var $el = $(el), table = $el.data('datatable');
+    if (table) table.columns.adjust();
+    $el.find('.dataTables_scrollHeadInner').css('width', '')
+        .children('table').css('margin-left', '');
+  }
+});
+
+  if (!HTMLWidgets.shinyMode) return;
+
+  Shiny.addCustomMessageHandler('datatable-calls', function(data) {
+    var id = data.id;
+    var el = document.getElementById(id);
+    var table = el ? $(el).data('datatable') : null;
+    if (!table) {
+      console.log("Couldn't find table with id " + id);
+      return;
+    }
+
+    var methods = table.shinyMethods, call = data.call;
+    if (methods[call.method]) {
+      methods[call.method].apply(table, call.args);
+    } else {
+      console.log("Unknown method " + call.method);
+    }
+  });
+
+})();
diff --git a/docs/articles/scFlow_files/dt-core-1.13.6/css/jquery.dataTables.extra.css b/docs/articles/scFlow_files/dt-core-1.13.6/css/jquery.dataTables.extra.css
new file mode 100644
index 0000000..b2dd141
--- /dev/null
+++ b/docs/articles/scFlow_files/dt-core-1.13.6/css/jquery.dataTables.extra.css
@@ -0,0 +1,28 @@
+/* Selected rows/cells */
+table.dataTable tr.selected td, table.dataTable td.selected {
+  background-color: #b0bed9 !important;
+}
+/* In case of scrollX/Y or FixedHeader */
+.dataTables_scrollBody .dataTables_sizing {
+  visibility: hidden;
+}
+
+/* The datatables' theme CSS file doesn't define
+the color but with white background. It leads to an issue that
+when the HTML's body color is set to 'white', the user can't
+see the text since the background is white. One case happens in the
+RStudio's IDE when inline viewing the DT table inside an Rmd file,
+if the IDE theme is set to "Cobalt".
+
+See https://github.com/rstudio/DT/issues/447 for more info
+
+This fixes should have little side-effects because all the other elements
+of the default theme use the #333 font color.
+
+TODO: The upstream may use relative colors for both the table background
+and the color. It means the table can display well without this patch
+then. At that time, we need to remove the below CSS attributes.
+*/
+div.datatables {
+  color: #333;
+}
diff --git a/docs/articles/scFlow_files/dt-core-1.13.6/css/jquery.dataTables.min.css b/docs/articles/scFlow_files/dt-core-1.13.6/css/jquery.dataTables.min.css
new file mode 100644
index 0000000..ad59f84
--- /dev/null
+++ b/docs/articles/scFlow_files/dt-core-1.13.6/css/jquery.dataTables.min.css
@@ -0,0 +1 @@
+:root{--dt-row-selected: 13, 110, 253;--dt-row-selected-text: 255, 255, 255;--dt-row-selected-link: 9, 10, 11;--dt-row-stripe: 0, 0, 0;--dt-row-hover: 0, 0, 0;--dt-column-ordering: 0, 0, 0;--dt-html-background: white}:root.dark{--dt-html-background: rgb(33, 37, 41)}table.dataTable td.dt-control{text-align:center;cursor:pointer}table.dataTable td.dt-control:before{display:inline-block;color:rgba(0, 0, 0, 0.5);content:"►"}table.dataTable tr.dt-hasChild td.dt-control:before{content:"▼"}html.dark table.dataTable td.dt-control:before{color:rgba(255, 255, 255, 0.5)}html.dark table.dataTable tr.dt-hasChild td.dt-control:before{color:rgba(255, 255, 255, 0.5)}table.dataTable thead>tr>th.sorting,table.dataTable thead>tr>th.sorting_asc,table.dataTable thead>tr>th.sorting_desc,table.dataTable thead>tr>th.sorting_asc_disabled,table.dataTable thead>tr>th.sorting_desc_disabled,table.dataTable thead>tr>td.sorting,table.dataTable thead>tr>td.sorting_asc,table.dataTable 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new file mode 100644
index 0000000..f786b0d
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