Commit 527dfef0 authored by Gervaise H. Henry's avatar Gervaise H. Henry 🤠

Include new colorsceme to all figs

parent e3622098
......@@ -100,10 +100,10 @@ sc10x.epi$`Cell Type` <- factor(sc10x.epi$`Cell Type`,levels=c("BE","Ur","VPr LE
Idents(sc10x.epi) <- "Cell Type"
postscript(paste0("./analysis/vis/diy/UMAP_epi.eps"))
DimPlot(sc10x.epi)+scale_color_viridis(discrete=TRUE)+theme_cowplot()
DimPlot(sc10x.epi)+scale_color_brewer(palette="Dark2")+theme_cowplot()
dev.off()
postscript(paste0("./analysis/vis/diy/UMAP_epi.split.eps"))
DimPlot(sc10x.epi,split.by="Region")+scale_color_viridis(discrete=TRUE)+theme_cowplot()
DimPlot(sc10x.epi,split.by="Region")+scale_color_brewer(palette="Dark2")+theme_cowplot()
dev.off()
Idents(sc10x.epi) <- "Region"
......@@ -116,7 +116,7 @@ postscript(paste0("./analysis/vis/diy/UMAP_epi.split.pr.eps"))
DimPlot(sc10x.epi.pr)+scale_color_brewer(palette="Dark2")+theme_cowplot()
dev.off()
postscript(paste0("./analysis/vis/diy/UMAP_epi.split.ur.eps"))
DimPlot(sc10x.epi.ur)+scale_color_viridis(discrete=TRUE)+theme_cowplot()
DimPlot(sc10x.epi.ur)+scale_color_brewer(palette="Dark2")+theme_cowplot()
dev.off()
labs.epi <- data.frame(ID=singler.epi$labels,`Cell Type`=c("APr LE","BE","Ur","VPr LE","ED","DLPr LE"),row.names=rownames(singler.epi))
......@@ -170,4 +170,4 @@ write.table(table(sc10x$`Cell Lineage`,sc10x$samples),file="./analysis/vis/diy/T
write.table(table(sc10x$`Cell Lineage`,sc10x$Region),file="./analysis/vis/diy/Table_Lin.Region.csv",sep=",",quote=FALSE,row.names=TRUE,col.names=NA)
write.table(table(sc10x.epi$`Cell Type`,sc10x.epi$samples),file="./analysis/vis/diy/Table_Epi.Samples.csv",sep=",",quote=FALSE,row.names=TRUE,col.names=NA)
write.table(table(sc10x.epi$`Cell Type`,sc10x.epi$Region),file="./analysis/vis/diy/Table_Epi.Region.csv",sep=",",quote=FALSE,row.names=TRUE,col.names=NA)
\ No newline at end of file
write.table(table(sc10x.epi$`Cell Type`,sc10x.epi$Region),file="./analysis/vis/diy/Table_Epi.Region.csv",sep=",",quote=FALSE,row.names=TRUE,col.names=NA)
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