From 57b870d11a1d2a7f585e9740af19caa8fd7663d8 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 2 Sep 2018 09:03:16 -0500
Subject: [PATCH] Remove downsampling from pseudotime and fix
---
r.scripts/sc-TissueMapper.R | 10 +++++-----
r.scripts/sc-TissueMapper_RUN.Pd.R | 4 +++-
2 files changed, 8 insertions(+), 6 deletions(-)
diff --git a/r.scripts/sc-TissueMapper.R b/r.scripts/sc-TissueMapper.R
index b41269c..db19abd 100644
--- a/r.scripts/sc-TissueMapper.R
+++ b/r.scripts/sc-TissueMapper.R
@@ -1222,10 +1222,10 @@ scCustHeatmap <- function(sc10x,i,gs,g){
scPseudotime <- function(sc10x,i,ds){
sc10x <- SetAllIdent(object=sc10x,id=i)
- if (ncol(sc10x@data)>ds){
+ if (ncol(sc10x@data)<ds){
rnd <- sample(1:ncol(sc10x@data),ds)
sc10x <- SetIdent(object=sc10x,cells.use=sc10x@data@Dimnames[[2]][rnd],ident.use="sample")
- sc10x <- SubsetData(object=sc10x,ident.use="sample")
+ sc10x <- SubsetData(object=sc10x,ident.use="samples")
sc10x <- SetAllIdent(object=sc10x,id=i)
}
scMonocle <- importCDS(sc10x)
@@ -1262,9 +1262,9 @@ scPseudotime <- function(sc10x,i,ds){
my_pseudotime_cluster <- plot_pseudotime_heatmap(scMonocle[gene_to_cluster,],show_rownames=TRUE,return_heatmap=TRUE)
dev.off()
- BEAM_res <- BEAM(scMonocle,branch_point=1,cores=50)
- BEAM_res <- BEAM_res[order(BEAM_res$qval),]
- BEAM_res <- BEAM_res[,c("gene_short_name","pval","qval")]
+ #BEAM_res <- BEAM(scMonocle,branch_point=1,cores=50)
+ #BEAM_res <- BEAM_res[order(BEAM_res$qval),]
+ #BEAM_res <- BEAM_res[,c("gene_short_name","pval","qval")]
#plot_genes_branched_heatmap(scMonocle[rownames(subset(BEAM_res,qval<1e-4)),],branch_point=1,num_clusters=5,cores=50,use_gene_short_name=TRUE,show_rownames=TRUE)
}
diff --git a/r.scripts/sc-TissueMapper_RUN.Pd.R b/r.scripts/sc-TissueMapper_RUN.Pd.R
index d02030a..9e3fcff 100644
--- a/r.scripts/sc-TissueMapper_RUN.Pd.R
+++ b/r.scripts/sc-TissueMapper_RUN.Pd.R
@@ -421,12 +421,14 @@ for (g in c("Fib","SM","Endo","Leu")){
for (g in c("D17","D27","D35")){
sctSNEHighlight(sc10x,i="patient",g=g,file="D")
}
+sctSNEHighlight(sc10x,i="Pz",g="Pz",file="D")
+sctSNEHighlight(sc10x,i="Tz",g="Tz",file="D")
rm(g)
scCustHeatmap(sc10x.Epi,i="Epi.dws.sub",gs=c(genes.deg.BE.unique,genes.deg.LE.unique,genes.deg.OE1.unique,genes.deg.OE2.unique),g=c("BE","LE","OE1","OE2"))
scCustHeatmap(sc10x.St,i="St.go",gs=c(genes.deg.Fib.unique,genes.deg.SM.unique,genes.deg.Endo.unique,genes.deg.OE2.unique,genes.deg.Leu.unique),g=c("Fib","SM","Endo","Leu"))
-scPseudotime(sc10x.Epi,i="Epi.dws.sub",ds=10000)
+scPseudotime(sc10x.Epi,i="Epi.dws.sub",ds=0)
save(list=ls(pattern="sc10x.Stress"),file="./analysis/sc10x.Stress.Rda")
rm(list=ls(pattern="sc10x.Stress"))
--
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