Specify assay and slot for QUSAGE

r.scripts/sc-TissueMapper_functions.R

@@ -824,7 +824,7 @@ scQuSAGE <- function(sc10x,gs,save=FALSE,type,id,ds=0,nm="pops",print="tsne"){
     }
     cell.sample <- c(cell.sample,cell)
   }
-  data <- as.data.frame(as.matrix(GetAssayData(sc10x[,colnames(sc10x) %in% cell.sample])))
+  data <- as.data.frame(as.matrix(GetAssayData(sc10x[,colnames(sc10x) %in% cell.sample],assay="SCT",slot="scale.data")))
   labels <- labels[colnames(sc10x) %in% cell.sample]
   #groups <- sort(unique(labels))
   groups <- paste0("Cluster_",levels(sc10x@active.ident))