update to 0.7.4

DESCRIPTION

@@ -47,14 +47,15 @@ Language: en-US
 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),
@@ -69,13 +70,11 @@ Imports:
     ggpubr (>= 0.5.0),
     ggrepel (>= 0.9.2),
     ggridges (>= 0.5.4),
-    igraph,
     kBET (>= 0.99.6),
     leaflet (>= 2.1.1),
     limma (>= 3.54.0),
     magrittr (>= 2.0.3),
     MAST (>= 1.24.0),
-    Matrix,
     lme4,
     methods,
     monocle3 (>= 1.3.1),
@@ -113,8 +112,5 @@ Remotes:
     cole-trapnell-lab/monocle3,
     theislab/kBET,
     jlmelville/uwot,
-    hhoeflin/hdf5r,
-    ropensci/bib2df,
-    bzhanglab/WebGestaltR,
-    cran/riverplot
+    ropensci/bib2df
 VignetteBuilder: knitr

Dockerfile

@@ -112,6 +112,7 @@ RUN pip install stratocumulus \
 
 
 RUN install2.r -e -t source \
+Matrix \
 argparse \
 assertthat \
 BiocManager \
@@ -141,7 +142,6 @@ ids \
 knitr \
 leaflet \
 magrittr \
-Matrix \
 lme4 \
 igraph \
 paletteer \
@@ -179,6 +179,8 @@ tidyverse \
 UpSetR \
 utils \
 vroom \
+WebGestaltR \
+apcluster \
 && rm -rf /tmp/downloaded_packages
 
 ## Install Bioconductor packages
@@ -194,13 +196,9 @@ 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

NEWS.md

@@ -1,5 +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.

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),

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

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.

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