Merge branch 'master' of https://github.com/ncborcherding/scRepertoire

BorchLab · Dec 21, 2023 · ce55335 · ce55335
2 parents db13d42 + 14b7a82
commit ce55335
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Showing 4 changed files with 9 additions and 9 deletions.
diff --git a/R/combineExpression.R b/R/combineExpression.R
@@ -76,7 +76,7 @@ combineExpression <- function(input.data,
     Con.df <- NULL
     meta <- .grabMeta(sc.data)
     cell.names <- rownames(meta)
-    if (group.by == "none" || is.null(group.by)) {
+    if (is.null(group.by) || group.by == "none") {
         for (i in seq_along(input.data)) {
 
             data <- data.frame(input.data[[i]], stringsAsFactors = FALSE)
@@ -104,7 +104,7 @@ combineExpression <- function(input.data,
         )
 
         colnames(data2)[c(1,2)] <- c(cloneCall, group.by)
-        data <- merge(data, data2, by = cloneCall, all = TRUE)
+        data <- merge(data, data2, by = c(cloneCall, group.by), all = TRUE)
         Con.df <- data[,c("barcode", "CTgene", "CTnt", 
                           "CTaa", "CTstrict", "clonalProportion", 
                           "clonalFrequency")]

diff --git a/index.md b/index.md
@@ -38,7 +38,7 @@ Unfortunately, Github limits the size of individual files. In order to access th
 
 We are working on submitting the scRepertoire as a peer review article, for now: 
 
-***Borcherding, N. & Wang, Q. 2023. scRepertoire v2: Expanded toolkit for single-cell immune repertoire analysis***
+***Borcherding, N. & Yang, Q. 2023. scRepertoire v2: Expanded toolkit for single-cell immune repertoire analysis***
 
 ## Bug Reports/New Features
 

diff --git a/inst/pkgdown.yml b/inst/pkgdown.yml
@@ -17,8 +17,7 @@ articles:
   Repertoire_Summary: Repertoire_Summary.html
   SC_Visualizations: SC_Visualizations.html
   Trex: Trex.html
-  Trex_Trajectory: Trex_Trajectory.html
-last_built: 2023-11-17T15:37Z
+last_built: 2023-12-13T21:18Z
 urls:
   reference: https://www.borch.dev/uploads/scRepertoire/reference
   article: https://www.borch.dev/uploads/scRepertoire/articles

diff --git a/vignettes/articles/SC_Visualizations.Rmd b/vignettes/articles/SC_Visualizations.Rmd
@@ -129,15 +129,16 @@ head(shared.clones)
 
 ## highlightClones
 
-We can also look at the clonotypes by calling specific sequences in the `highlightClonotypes()` below. In order to highlight the clonotypes, we first need to use the **cloneCall**, the type of sequence we will be using, and then the specific sequences themselves using **sequence**. Below, we can see the steps to highlight the two most prominent sequences *"CVVSDNTGGFKTIF_CASSVRRERANTGELFF"* and *"NA_CASSVRRERANTGELFF"*.
+We can also look at the clonotypes by calling specific sequences in the `highlightClonotypes()` below. In order to highlight the clonotypes, we first need to use the **cloneCall**, the type of sequence we will be using, and then the specific sequences themselves using **sequence**. Below, we can see the steps to highlight the most prominent sequences *CAERGSGGSYIPTF_CASSDPSGRQGPRWDTQYF*, and *CARKVRDSSYKLIF_CASSDSGYNEQFF*.
 
 ```{r tidy = FALSE}
 scRep_example <- highlightClones(scRep_example, 
                     cloneCall= "aa", 
-                    sequence = c("CVVSDNTGGFKTIF_CASSVRRERANTGELFF", 
-                                 "NA_CASSVRRERANTGELFF"))
+                    sequence = c("CAERGSGGSYIPTF_CASSDPSGRQGPRWDTQYF", 
+                                 "CARKVRDSSYKLIF_CASSDSGYNEQFF"))
 
-Seurat::DimPlot(scRep_example, group.by = "highlight") 
+Seurat::DimPlot(scRep_example, group.by = "highlight") + 
+  ggplot2::theme(plot.title = element_blank())
 ```
 
 ## clonalOccupy