Merge pull request #410 from ncborcherding/dev

v2.0.7

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: scRepertoire
 Title: A toolkit for single-cell immune receptor profiling
-Version: 2.0.6
+Version: 2.0.7
 Authors@R: c(
     person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "[email protected]"), 
     person(given = "Qile", family = "Yang", role = c("aut"), email = "[email protected]"), 

NEWS.md

@@ -1,3 +1,9 @@
+# scRepertoire VERSION 2.0.7
+
+## UNDERLYING CHANGES
+* Fixed issue with "group.by" in ```clonalOverlap()```
+* Fixed issue with "group.by" in ```clonalCompare()```
+
 # scRepertoire VERSION 2.0.6
 
 ## UNDERLYING CHANGES

R/clonalCompare.R

@@ -74,6 +74,11 @@ clonalCompare <- function(input.data,
                               chain)
   cloneCall <- .theCall(input.data, cloneCall)
 
+  sco <- is_seurat_object(input.data) | is_se_object(input.data)
+  if(!is.null(group.by) & !sco) {
+    input.data <- .groupList(input.data, group.by)
+  }
+
   Con.df <- NULL
 
   #Loop through the list to get a proportional summary

R/clonalOverlap.R

@@ -89,6 +89,11 @@ clonalOverlap <- function(input.data,
     }
 
     cloneCall <- .theCall(input.data, cloneCall)
+
+    sco <- is_seurat_object(input.data) | is_se_object(input.data)
+    if(!is.null(group.by) & !sco) {
+      input.data <- .groupList(input.data, group.by)
+    }
 
     num_samples <- length(input.data[])
     names_samples <- names(input.data)

R/clonalQuant.R

@@ -49,8 +49,8 @@ clonalQuant <- function(input.data,
                               .theCall(input.data, cloneCall, check.df = FALSE), 
                               chain)
   cloneCall <- .theCall(input.data, cloneCall)
+
   sco <- is_seurat_object(input.data) | is_se_object(input.data)
-
   if(!is.null(group.by) & !sco) {
     input.data <- .groupList(input.data, group.by)
   }