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Commit 161e2414 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix NE score from using stress score

parent e86b3163
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......@@ -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)
......
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