clonalOccupy NA include argument fix

#337

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: scRepertoire
 Title: A toolkit for single-cell immune receptor profiling
-Version: 2.0.1
+Version: 2.0.2
 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

@@ -1,10 +1,14 @@
+# scRepertoire VERSION 2.0.2
+
+## UNDERLYING CHANGES
+
+*```clonalOccupy()``` rewrite counting and NA handling
+
 # scRepertoire VERSION 2.0.1 
 
 ## UNDERLYING CHANGES
 
 *```clonalOverlay()``` arguments now cutpoint and use cut.category to select either clonalProportion or clonalFrequency
-* ```clonalOccupy()``` allow NA calls
-
 
 # scRepertoire VERSION 2.0.0 (2024-01-10)
 

R/clonalOccupy.R

@@ -33,7 +33,7 @@
 #' environment in addition to the visualization.
 #' @param palette Colors to use in visualization - input any 
 #' \link[grDevices]{hcl.pals}.
-#' @importFrom dplyr %>% group_by mutate
+#' @importFrom dplyr %>% group_by mutate count
 #' @importFrom reshape2 melt
 #' @import ggplot2
 #' @export
@@ -50,20 +50,29 @@ clonalOccupy <- function(sc.data,
                          palette = "inferno") {
   .checkSingleObject(sc.data)
   meta <- .grabMeta(sc.data)
-  meta <- melt(table(meta[(meta[,"clonalFrequency"]), 
-                          c(x.axis, facet.by, "cloneSize")], useNA = "ifany"))
+
+  meta <- meta %>%
+            group_by(meta[,x.axis], meta[,facet.by], cloneSize) %>%
+            count() %>%
+            as.data.frame()
+
+  colnames(meta)[1] <- x.axis
+  if(!is.null(facet.by)) {
+    colnames(meta)[2] <- facet.by
+  }
+
   #Check for NAs
   if (!na.include) {
     meta <- na.omit(meta)
   }
-  meta <- meta[meta$value != 0,]
+  meta <- meta[meta$n != 0,]
 
   #Convert to proportion
   if(proportion) {
     meta <- meta %>%
       group_by(meta[,1]) %>%
-      mutate(total = sum(value), 
-             prop = value/total)
+      mutate(total = sum(n), 
+             prop = n/total)
     meta <- as.data.frame(meta)
   }
   if (exportTable) {
@@ -77,7 +86,7 @@ clonalOccupy <- function(sc.data,
     lab <- "Proportion of Cells"
 
   } else {
-    plot <- ggplot(meta, aes(x = meta[,x.axis], y = value, fill = cloneSize)) + 
+    plot <- ggplot(meta, aes(x = meta[,x.axis], y = n, fill = cloneSize)) + 
               geom_bar(stat = "identity", color = "black", lwd = 0.25) 
     lab <- "Single Cells"
 
@@ -94,7 +103,7 @@ clonalOccupy <- function(sc.data,
   }
   if (label) {
     plot <- plot + 
-              geom_text(aes(label = value), position = position_stack(vjust = 0.5))
+              geom_text(aes(label = n), position = position_stack(vjust = 0.5))
   }
   plot
 }

vignettes/articles/SC_Visualizations.Rmd

@@ -88,7 +88,7 @@ This visualization was authored by Dr. Francesco Mazziotta and inspired by Drs.
 ```{r tidy = FALSE}
 clonalOverlay(scRep_example, 
               reduction = "umap", 
-              freq.cutpoint = 1, 
+              cutpoint = 1, 
               bins = 10, 
               facet.by = "Patient") + 
               guides(color = "none")
@@ -129,7 +129,6 @@ clonalNetwork(scRep_example,
               filter.clones = NULL,
               filter.identity = NULL,
               cloneCall = "aa")
-
 ```
 
 We can look at the clonal relationships relative to a single cluster using the **filter.identity** parameter. 
@@ -185,9 +184,9 @@ clonalOccupy(scRep_example,
               x.axis = "seurat_clusters")
 
 clonalOccupy(scRep_example, 
-                     x.axis = "ident", 
-                     proportion = TRUE, 
-                     label = FALSE)
+             x.axis = "ident", 
+             proportion = TRUE, 
+             label = FALSE)
 ```
 
 ## alluvialClones

vignettes/vignette.Rmd

@@ -996,9 +996,9 @@ clonalOccupy(scRep_example,
               x.axis = "seurat_clusters")
 
 clonalOccupy(scRep_example, 
-                     x.axis = "ident", 
-                     proportion = TRUE, 
-                     label = FALSE)
+             x.axis = "ident", 
+             proportion = TRUE, 
+             label = FALSE)
 ```
 
 ## alluvialClones