Merge pull request #321 from ncborcherding/dev

Update pkgdown page
ncborcherding · Feb 24, 2024 · 6a919b9 · 6a919b9
2 parents e51695a + 427f525
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Showing 12 changed files with 515 additions and 14 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -27,7 +27,7 @@
 * **.theCall()** now allows for a custom header/variable and checks the colnames. 
 * Replaced data arguments to be more descriptive: *df* is now *input.data*, *dir* is now *input*, and *sc* is now *sc.data*
 * Deep clean on the documentation for each function for increased consistency and explainability
-* ```Startracdiversity()``` metric re-implemented to remove startrac-class object intermediary
+* ```StartracDiversity()``` metric re-implemented to remove startrac-class object intermediary
 * Implemented powerTCR locally to reduce dependencies and continue support
 * Universalized underlying function language and intermediate variables
 * License change to MIT

diff --git a/R/positionalProperty.R b/R/positionalProperty.R
@@ -67,7 +67,7 @@ positionalProperty <- function(input.data,
     input.data <- .groupList(input.data, group.by)
   }
 
-  #Selecting Diversit Function
+  #Selecting Property Function
   propertyFunc <- switch(method,
                           "Atchley" = .af.ref,
                           "Kidera" = .kf.ref,

diff --git a/README.md b/README.md
@@ -29,7 +29,7 @@ devtools::install_github("ncborcherding/scRepertoire")
 ```
 
 ### Installing from Bioconductor
-The current version of scRepertoire is also available in the development version of Bioconductor. Important to note, the version is listed as 1.99.0 on [Bioconductor](https://bioconductor.org/packages/3.19/bioc/html/scRepertoire.html) per their version guidelines.
+The current version of scRepertoire is also available in the development version of Bioconductor. Important to note, the version is listed as 1.99.1 on [Bioconductor](https://bioconductor.org/packages/3.19/bioc/html/scRepertoire.html) per their version guidelines.
 
 ```R
 BiocManager::install(version='devel')

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -51,6 +51,8 @@ navbar:
       href: articles/Trex.html
     - text: Combining Deep Learning and BCRs with Ibex
       href: articles/Ibex.html
+    - text: Single-cell Gene Set Enrichment Analysis
+      href: articles/Running_Escape.html
   - text: News/Changelog
     href: news/index.html
   - text: Reference
@@ -89,6 +91,7 @@ reference:
 - contents:
   - percentAA
   - positionalEntropy
+  - positionalProperty
   - percentGenes
   - percentKmer
   - percentVJ

diff --git a/inst/pkgdown.yml b/inst/pkgdown.yml
@@ -15,9 +15,10 @@ articles:
   Loading: Loading.html
   Processing: Processing.html
   Repertoire_Summary: Repertoire_Summary.html
+  Running_Escape: Running_Escape.html
   SC_Visualizations: SC_Visualizations.html
   Trex: Trex.html
-last_built: 2024-01-22T10:54Z
+last_built: 2024-02-24T16:17Z
 urls:
   reference: https://www.borch.dev/uploads/scRepertoire/reference
   article: https://www.borch.dev/uploads/scRepertoire/articles

diff --git a/vignettes/articles/Attaching_SC.Rmd b/vignettes/articles/Attaching_SC.Rmd
@@ -45,8 +45,6 @@ data("contig_list")
 combined.TCR <- combineTCR(contig_list, 
                            samples = c("P17B", "P17L", "P18B", "P18L", 
                                             "P19B","P19L", "P20B", "P20L"))
-
-googledrive::drive_download("https://drive.google.com/file/d/1_YuRraDyg8UgF3oasjF0-jgPnwox-B24/view?usp=share_link", overwrite = TRUE)
 ```
 
 The data in the scRepertoire package is derived from a [study](https://pubmed.ncbi.nlm.nih.gov/33622974/) of acute respiratory stress disorder in the context of bacterial and COVID-19 infections. The internal single cell data (`scRep_example()`) built in to scRepertoire is randomly sampled 500 cells from the fully integrated Seurat object to minimize the package size. However, for the purpose of the vignette we will use the full single-cell object with 30,000 cells. We will use both Seurat and Single-Cell Experiment (SCE) with scater to perform further visualizations in tandem. 

diff --git a/vignettes/articles/Clonal_Cluster.Rmd b/vignettes/articles/Clonal_Cluster.Rmd
@@ -42,9 +42,7 @@ suppressMessages(library(Seurat))
 data("contig_list") 
 combined.TCR <- combineTCR(contig_list, 
                            samples = c("P17B", "P17L", "P18B", "P18L", 
-                                            "P19B","P19L", "P20B", "P20L"))
-
-googledrive::drive_download("https://drive.google.com/file/d/1_YuRraDyg8UgF3oasjF0-jgPnwox-B24/view?usp=share_link", overwrite = TRUE)
+                                       "P19B","P19L", "P20B", "P20L"))
 
 scRep_example <- readRDS("scRep_example_full.rds")
 

diff --git a/vignettes/articles/Ibex.Rmd b/vignettes/articles/Ibex.Rmd
@@ -37,7 +37,7 @@ knitr::opts_chunk$set(
   time_it = TRUE
 )
 suppressMessages(library(reticulate))
-use_condaenv(condaenv = "r-reticulate", required = TRUE)
+#use_condaenv(condaenv = "r-reticulate", required = TRUE)
 suppressMessages(library(Ibex))
 suppressMessages(library(Seurat))
 suppressMessages(library(ggplot2))

diff --git a/vignettes/articles/Installation.Rmd b/vignettes/articles/Installation.Rmd
@@ -55,9 +55,9 @@ remotes::install_github(repo = "ncborcherding/scRepertoire", ref = "dev")
 
 ## Bioconductor
 
-The current version of scRepertoire is also available in the development version of Bioconductor. Important to note, the version is listed as 1.99.0 on [Bioconductor](https://bioconductor.org/packages/3.19/bioc/html/scRepertoire.html) per their version guidelines.
+The current version of scRepertoire is also available in the development version of Bioconductor. Important to note, the version is listed as 1.99.1 on [Bioconductor](https://bioconductor.org/packages/3.19/bioc/html/scRepertoire.html) per their version guidelines.
 
-```{r}
+```
 BiocManager::install(version='devel')
 
 BiocManager::install("scRepertoire")