Fix NE score from using stress score

r.scripts/sc-TissueMapper.R

@@ -816,7 +816,7 @@ scNE <- function(sc10x,neg="EurUro",cut=0.95){
   sc10x <- SetDimReduction(object=sc10x,reduction.type="NE",slot="cell.embeddings",new.data=sc10x.NE.pca)
   sc10x <- SetDimReduction(object=sc10x,reduction.type="NE",slot="key",new.data="NE")
   
-  #Generate PCA PC1 (Stress1/Stress-Score) and PC2 (Stress2)
+  #Generate PCA PC1 (NE1/NE-Score) and PC2 (NE2)
   postscript("./analysis/pca/ne/PCA.eps")
   plot <- DimPlot(object=sc10x,reduction.use="NE",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
   plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
@@ -824,15 +824,15 @@ scNE <- function(sc10x,neg="EurUro",cut=0.95){
   plot(plot)
   dev.off()
   
-  #CDS
-  cdf <- ecdf(GetCellEmbeddings(object=sc10x,reduction.type="Stress",dims.use=1))
+  #CDF
+  cdf <- ecdf(GetCellEmbeddings(object=sc10x,reduction.type="NE",dims.use=1))
   cut.x <- quantile(cdf,probs=cut)
   postscript("./analysis/pca/ne/CDF_NE.eps")
-  plot(cdf,main="Cumulative Distribution of Stress Score",xlab="Stress Score",ylab="CDF")
+  plot(cdf,main="Cumulative Distribution of NE Score",xlab="NE Score",ylab="CDF")
   abline(v=cut.x,col="red")
   dev.off()
   
-  #Find first turning point on a KDE of Stress1
+  #Find first turning point on a KDE of NE1
   postscript("./analysis/pca/ne/Histo_NE.eps")
   histo <- hist(GetCellEmbeddings(object=sc10x,reduction.type="NE",dims.use=1),breaks=100,probability=TRUE,plot=TRUE)
   d1 <- density(GetCellEmbeddings(object=sc10x,reduction.type="NE",dims.use=1),n=100)