Change ribo lower cutoff to 10% and change thresh scale to 0-255

r.scripts/sc-TissueMapper_functions.R

@@ -289,7 +289,7 @@ scQC <- function(sc10x,sp="hu",feature="nFeature_RNA"){
           cutoff.l <- 0
         } else if (i == "percent.ribo") {
           cutoff.h <- max(sc10x[[j]][[i]])
-          cutoff.l <- thresh[[i]][[j]]$threshold[thresh[[i]][[j]]$method=="RenyiEntropy"]
+          cutoff.l <- 10
         } else if (i == "nCount_RNA") {
           cutoff.h <- max(sc10x[[j]][[i]])
           cutoff.l <- thresh[[i]][[j]]$threshold[thresh[[i]][[j]]$method=="RenyiEntropy"]
@@ -425,12 +425,12 @@ scThresh <- function(sc10x,feature,sub=FALSE){
     scale[[i]] <- data.frame(Score=sc10x[[i]][[feature]])
     colnames(scale[[i]]) <- "Score"
     scale[[i]] <- data.frame(Score=scale[[i]]$Score[!is.na(scale[[i]]$Score)])
-    scale.scaled[[i]] <- as.integer((scale[[i]]$Score-min(scale[[i]]$Score))/(max(scale[[i]]$Score)-min(scale[[i]]$Score))*360)
+    scale.scaled[[i]] <- as.integer((scale[[i]]$Score-min(scale[[i]]$Score))/(max(scale[[i]]$Score)-min(scale[[i]]$Score))*255)
     #scale.scaled[[i]] <- as.integer(scales::rescale(scale[[i]]$Score,to=c(0,1))*360)
     h[[i]] <- hist(scale[[i]]$Score,breaks=100,plot=FALSE)
     thresh[[i]] <- purrr::map_chr(thresh_methods,~auto_thresh(scale.scaled[[i]],.)) %>% tibble(method = thresh_methods, threshold = .)
     thresh[[i]]$threshold <- as.numeric(thresh[[i]]$threshold)
-    thresh[[i]]$threshold <- ((thresh[[i]]$threshold/360)*(max(scale[[i]]$Score)-min(scale[[i]]$Score)))+min(scale[[i]]$Score)
+    thresh[[i]]$threshold <- ((thresh[[i]]$threshold/255)*(max(scale[[i]]$Score)-min(scale[[i]]$Score)))+min(scale[[i]]$Score)
     #thresh[[i]] <- thresh[[i]] %>% mutate(threshold=(scales::rescale(as.numeric(threshold)/360,to=range(scale[[i]]$Score))))
     postscript(paste0(folder,"Hist_qc.",i,".",feature,".eps"))
     plot(h[[i]],main=paste0("Histogram of ",feature," of sample ",i),xlab=feature)