Remove tsne plotting from ID

r.scripts/sc-TissueMapper_ID.R

@@ -118,11 +118,11 @@ if (ncol(sc10x.epi) > 1000) {
 } else if (ncol(sc10x.epi) > 100) {
   pc.calc.epi <- ncol(sc10x.epi)-1
 }
-results <- scPC(sc10x.epi,pc=pc.calc.epi,hpc=0.9,file="epi",print="2")
+results <- scPC(sc10x.epi,pc=pc.calc.epi,hpc=0.9,file="epi",print="umap")
 sc10x.epi <- results[[1]]
 pc.use.epi <- results[[2]]
 rm(results)
-sc10x.epi <- scCluster(sc10x.epi,res=res,red="pca",dim=pc.use.epi,print="2",folder="epi")
+sc10x.epi <- scCluster(sc10x.epi,res=res,red="pca",dim=pc.use.epi,print="umap",folder="epi")
 #DimPlot(sc10x.epi,group.by="integrated_snn_res.0.1",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
 
 if (ncol(sc10x.fmst) > 1000) {
@@ -132,11 +132,11 @@ if (ncol(sc10x.fmst) > 1000) {
 } else if (ncol(sc10x.fmst) > 100) {
   pc.calc.fmst <- ncol(sc10x.fmst)-1
 }
-results <- scPC(sc10x.fmst,pc=pc.calc.fmst,hpc=0.9,file="fmst",print="2")
+results <- scPC(sc10x.fmst,pc=pc.calc.fmst,hpc=0.9,file="fmst",print="umap")
 sc10x.fmst <- results[[1]]
 pc.use.fmst <- results[[2]]
 rm(results)
-sc10x.fmst <- scCluster(sc10x.fmst,res=res,red="pca",dim=pc.use.fmst,print="2",folder="fmst")
+sc10x.fmst <- scCluster(sc10x.fmst,res=res,red="pca",dim=pc.use.fmst,print="umap",folder="fmst")
 #DimPlot(sc10x.fmst,group.by="integrated_snn_res.0.1",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
 
 if (ncol(sc10x.fib) > 1000) {
@@ -146,11 +146,11 @@ if (ncol(sc10x.fib) > 1000) {
 } else if (ncol(sc10x.fib) > 100) {
   pc.calc.fib <- ncol(sc10x.fib)-1
 }
-results <- scPC(sc10x.fib,pc=pc.calc.fib,hpc=0.9,file="all",print="2")
+results <- scPC(sc10x.fib,pc=pc.calc.fib,hpc=0.9,file="all",print="umap")
 sc10x.fib <- results[[1]]
 pc.use.fib <- results[[2]]
 rm(results)
-sc10x.fib <- scCluster(sc10x.fib,res=res,red="pca",dim=pc.use.fib,print="2",folder="fib")
+sc10x.fib <- scCluster(sc10x.fib,res=res,red="pca",dim=pc.use.fib,print="umap",folder="fib")
 #DimPlot(sc10x.fib,group.by="integrated_snn_res.0.1",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
 
 if (ncol(sc10x.sm) > 1000) {
@@ -160,11 +160,11 @@ if (ncol(sc10x.sm) > 1000) {
 } else if (ncol(sc10x.sm) > 100) {
   pc.calc.sm <- ncol(sc10x.sm)-1
 }
-results <- scPC(sc10x.sm,pc=pc.calc.sm,hpc=0.9,file="sm",print="2")
+results <- scPC(sc10x.sm,pc=pc.calc.sm,hpc=0.9,file="sm",print="umap")
 sc10x.sm <- results[[1]]
 pc.use.sm <- results[[2]]
 rm(results)
-sc10x.sm <- scCluster(sc10x.sm,res=res,red="pca",dim=pc.use.sm,print="2",folder="sm")
+sc10x.sm <- scCluster(sc10x.sm,res=res,red="pca",dim=pc.use.sm,print="umap",folder="sm")
 #DimPlot(sc10x.sm,group.by="integrated_snn_res.0.1",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
 
 if (ncol(sc10x.leu) > 1000) {
@@ -174,11 +174,11 @@ if (ncol(sc10x.leu) > 1000) {
 } else if (ncol(sc10x.leu) > 100) {
   pc.calc.leu <- ncol(sc10x.leu)-1
 }
-results <- scPC(sc10x.leu,pc=pc.calc.leu,hpc=0.9,file="leu",print="2")
+results <- scPC(sc10x.leu,pc=pc.calc.leu,hpc=0.9,file="leu",print="umap")
 sc10x.leu <- results[[1]]
 pc.use.leu <- results[[2]]
 rm(results)
-sc10x.leu <- scCluster(sc10x.leu,res=res,red="pca",dim=pc.use.leu,print="2",folder="leu")
+sc10x.leu <- scCluster(sc10x.leu,res=res,red="pca",dim=pc.use.leu,print="umap",folder="leu")
 #DimPlot(sc10x.leu,group.by="integrated_snn_res.0.1",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
 
 if (opt$o == "pr" && opt$s == "hu") {