Change Stress cell determination back to PC1

r.scripts/sc_PC.Score.Stress.R

@@ -65,7 +65,7 @@ if (skewness(sc10x.Group.Stress.pca[,2])<0){
 sc10x.Group <- SetDimReduction(object=sc10x.Group,reduction.type="Stress",slot="cell.embeddings",new.data=sc10x.Group.Stress.pca)
 sc10x.Group <- SetDimReduction(object=sc10x.Group,reduction.type="Stress",slot="key",new.data="Stress")
 
-#generate PCA PC1 (Stress1) and PC2 (Stress2)
+#generate PCA PC1 (Stress1/Stress-Score) and PC2 (Stress2)
 postscript(paste0("./analysis/",opt$g,"/pc-score/PCS_Stress.eps"))
 plot <- DimPlot(object=sc10x.Group,reduction.use="Stress",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
 plot <- plot+geom_density2d(color="black",bins=25,alpha=0.5)
@@ -74,19 +74,19 @@ plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
 plot(plot)
 dev.off()
 
-#find first turning point on a KDE of Stress1 & Stress2
+#find first turning point on a KDE of Stress1
 d1 <- density(GetCellEmbeddings(object=sc10x.Group,reduction.type="Stress",dims.use=1),n=1000)
-d2 <- density(GetCellEmbeddings(object=sc10x.Group,reduction.type="Stress",dims.use=2),n=1000)
+#d2 <- density(GetCellEmbeddings(object=sc10x.Group,reduction.type="Stress",dims.use=2),n=1000)
 ts_1 <- ts(d1$y)
-ts_2 <- ts(d2$y)
+#ts_2 <- ts(d2$y)
 tp1 <- turnpoints(ts_1)
-tp2 <- turnpoints(ts_2)
+#tp2 <- turnpoints(ts_2)
 pit1 <- min(d1$x[tp1$pits])
-pit2 <- min(d2$x[tp2$pits])
+#pit2 <- min(d2$x[tp2$pits])
 
 #plot clusters
 ALL <- GetCellEmbeddings(object=sc10x.Group,reduction.type="Stress",dims.use=1:2)
-Stress <- rownames(ALL[ALL[,1]>pit1 | ALL[,2]>pit2,])
+Stress <- rownames(ALL[ALL[,1]>pit1)
 sc10x.Group <- SetAllIdent(object=sc10x.Group,id="ALL")
 sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=Stress,ident.use="Stress")
 postscript(paste0("./analysis/",opt$g,"/pc-score/PCS_Stress.Group.eps"))