Add dynamic component calculation based on cell number (RAW)

r.scripts/sc-TissueMapper_RAW.R

@@ -70,7 +70,12 @@ pc.use.prestress <- list()
 for (i in names(sc10x)){
   sc10x.temp <- sc10x[[i]]
   sc10x.temp <- SCTransform(sc10x.temp,vars.to.regress=c("nFeature_RNA","percent.mito"),verbose=FALSE,assay="RNA")
-  results <- scPC(sc10x.temp,pc=100,hpc=0.9,file=paste0(i,".pre.stress"),print="2",assay="SCT")
+  if (ncol(sc10x.temp) > 100) {
+    pc.calc <- 100
+  } else if (ncol(sc10x.temp) <= 100) {
+    pc.calc <- ncol(sc10x.temp)-1
+  }
+  results <- scPC(sc10x.temp,pc=pc.calc,hpc=0.9,file=paste0(i,".pre.stress"),print="2",assay="SCT")
   sc10x.temp <- results[[1]]
   pc.use.prestress.temp <- results[[2]]
   rm(results)
@@ -78,6 +83,7 @@ for (i in names(sc10x)){
   sc10x[i] <- sc10x.temp
   pc.use.prestress[i] <- pc.use.prestress.temp
   rm(sc10x.temp)
+  rm(pc.calc)
   rm(pc.use.prestress.temp)
 }
 rm(i)
@@ -129,10 +135,18 @@ if (length(sc10x)>1){
 }
 gc()
 
-results <- scPC(sc10x,pc=1000,hpc=0.9,file="ALL",print="2")
+if (ncol(sc10x) > 1000) {
+  pc.calc <- 1000
+} else if (ncol(sc10x) > 500) {
+  pc.calc <- 500
+} else if (ncol(sc10x) > 100) {
+  pc.calc <- ncol(sc10x)-1
+}
+results <- scPC(sc10x,pc=pc.calc,hpc=0.9,file="ALL",print="2")
 sc10x <- results[[1]]
 pc.use.poststress <- results[[2]]
 rm(results)
+rm(pc.calc)
 
 res <- c(seq(0.1,0.5,0.1),0.75,seq(1,5,1))