Change clustering to use integrated assay

r.scripts/sc-TissueMapper_functions.R

@@ -508,6 +508,8 @@ scCluster <- function(sc10x,res=0.1,red="pca",dim,print="tsne",folder=FALSE){
     
   }
   
+  DefaultAssay(sc10x) <- "integrated"
+
   #Calculste Vis
   sc10x <- RunTSNE(sc10x,dims=1:dim,reduction="pca",assay="integrated")
   sc10x <- RunUMAP(sc10x,dims=1:dim,reduction="pca",assay="integrated")
@@ -571,6 +573,8 @@ scCluster <- function(sc10x,res=0.1,red="pca",dim,print="tsne",folder=FALSE){
     grid.arrange(plot1,plot2,plot3,legend,ncol=1)
     dev.off()
   }
+
+  DefaultAssay(sc10x) <- "SCT"
   
   return(sc10x)
 }