Fix aggregation.csv file load for cellranger 3

r.scripts/sc-TissueMapper_functions.R

@@ -53,9 +53,17 @@ scLoad <- function(p,mc=3,mg=200,sub=FALSE,cellranger=3,ref="GRCh38"){
   
   #Label sample names from aggregation_csv.csv
   if (sub==FALSE){
-    sc10x.aggr <- read_csv("./analysis/DATA/10x/aggregation_csv.csv")
+    if (cellranger==2){
+      sc10x.aggr <- read_csv("./analysis/DATA/10x/aggregation_csv.csv")
+    } else {
+      sc10x.aggr <- read_csv("./analysis/DATA/10x/aggregation.csv")
+    }
   } else {
-    sc10x.aggr <- read_csv(paste0("./analysis/DATA/",p,"/10x/aggregation_csv.csv"))
+    if (cellranger==2){
+      sc10x.aggr <- read_csv(paste0("./analysis/DATA/",p,"/10x/aggregation_csv.csv"))
+    } else {
+      sc10x.aggr <- read_csv(paste0("./analysis/DATA/",p,"/10x/aggregation.csv"))
+    }
   }
   cell.codes <- as.data.frame(sc10x@raw.data@Dimnames[[2]])
   colnames(cell.codes) <- "barcodes"