Update qusage fncton

r.scripts/sc-TissueMapper_functions.R

@@ -852,7 +852,7 @@ scQuSAGE <- function(sc10x,gs,save=FALSE,type,id,ds=0,nm="pops",print="umap"){
     }
     cell.sample <- c(cell.sample,cell)
   }
-  data <- as.data.frame(as.matrix(GetAssayData(sc10x[,colnames(sc10x) %in% cell.sample],assay="SCT",slot="scale.data")))
+  data <- as.data.frame(as.matrix(GetAssayData(sc10x[,colnames(sc10x) %in% cell.sample],assay="SCT",slot="data")))
   labels <- labels[colnames(sc10x) %in% cell.sample]
   #groups <- sort(unique(labels))
   groups <- paste0("Cluster_",levels(sc10x@active.ident))
@@ -920,14 +920,14 @@ scQuSAGE <- function(sc10x,gs,save=FALSE,type,id,ds=0,nm="pops",print="umap"){
   max.y.rg <- 0
   for (i in groups){
     qs <- get(paste0("results.",i))
-    if (max(qs$path.mean)>max.x.rg){
-      max.x.rg <- max(qs$path.mean)
+    if (max(qs$path.mean[!is.nan(qs$path.mean)])>max.x.rg){
+      max.x.rg <- max(qs$path.mean[!is.nan(qs$path.mean)])
     }
-    if (min(qs$path.mean)<min.x.rg){
-      min.x.rg <- min(qs$path.mean)
+    if (min(qs$path.mean[!is.nan(qs$path.mean)])<min.x.rg){
+      min.x.rg <- min(qs$path.mean[!is.nan(qs$path.mean)])
     }
-    if (max(qs$path.PDF)>max.y.rg){
-      max.y.rg <- max(qs$path.PDF)
+    if (max(qs$path.PDF[!is.na(qs$path.PDF)])>max.y.rg){
+      max.y.rg <- max(qs$path.PDF[!is.na(qs$path.PDF)])
     }}
   if (type=="sm"){
     #Plot correlation plots by geneset