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Commit 71e4c555 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Remove depreciated D17 and D17+D27 workfolows

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r.scripts/sc-TissueMapper_RUN.D.diy.R deleted 100644 → 0
+ 0
− 153
View file @ 80d84d6b
gc()
library(methods)
library(optparse)
library(Seurat)
library(readr)
library(fBasics)
library(pastecs)
library(qusage)
library(RColorBrewer)
setwd("../")
load("./analysis/sc10x.Rda")
load("./analysis/sc10x.Stress.Rda")
load("./analysis/sc10x.Epi.Rda")
load("./analysis/sc10x.St.Rda")
load("./analysis/Data.RData")
load("./analysis/DEG.Rda")
source("./r.scripts/sc-TissueMapper.R")
sctSNECustCol(sc10x,i="Lin",bl="Epi",rd="St",file="Aggr")
sctSNECustCol(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",bl=c("BE","LE","OE_SCGB","OE_KRT13"),rd=c("Fib","SM","Endo","Leu"),file="Aggr")
sctSNECustCol(sc10x.Epi,i="Epi.dws.sc",bl=c("BE","LE","OE_SCGB","OE_KRT13"),rd="",file="Aggr")
sctSNECustCol(sc10x.St,i="St.dws.sc",bl="",rd=c("Fib","SM","Endo","Leu"),file="Aggr")
sctSNEbwCol(sc10x,i="res0.2",file="ALL",files="Aggr")
sctSNEbwCol(sc10x.Epi,i="res0.2",file="Epi",files="Aggr")
sctSNEbwCol(sc10x.St,i="res0.2",file="St",files="Aggr")
sctSNEbwCol(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",file="ALL",files="Aggr")
sctSNEbwCol(sc10x.Epi,i="Epi.dws.sc",file="Epi",files="Aggr")
sctSNEbwCol(sc10x.St,i="St.dws.sc",file="St",files="Aggr")
for (g in c("Epi","St")){
sctSNEHighlight(sc10x,i="Lin",g=g,file="Aggr")
}
for (g in c("BE","LE","OE_SCGB","OE_KRT13")){
sctSNEHighlight(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",g=g,file="Aggr")
sctSNEHighlight(sc10x.Epi,i="Epi.dws.sc",g=g,file="Aggr")
}
sctSNEHighlight(sc10x.Epi.NE,i="NE",g="NE",file="Aggr")
for (g in c("Fib","SM","Endo","Leu")){
sctSNEHighlight(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",g=g,file="Aggr")
sctSNEHighlight(sc10x.St,i="St.dws.sc",g=g,file="Aggr")
}
for (g in c("D17PrPzF_BE","D17PrPzF_LE","D17PrPzF_OE","D17PrPzF_FMSt","D17PrPzF_Via","D17PrTzF_Via","D27PrTzF_BE","D27PrTzF_LE","D27PrTzF_OE","D27PrTzF_Edn","D27PrTzF_StPDPNp","D27PrTzF_StPDPNn","D27PrPzF_Via","D27PrTzF_Via")){
sctSNEHighlight(sc10x,i="samples",g=g,file="Aggr")
}
rm(g)
scCustHeatmap(sc10x.Epi,i="Epi.dws.sub",gs=c(genes.deg.BE.unique,genes.deg.LE.unique,genes.deg.OE_SCGB.unique,genes.deg.OE_KRT13.unique),g=c("BE","LE","OE_SCGB","OE_KRT13"))
scCustHeatmap(sc10x.St,i="St.go",gs=c(genes.deg.Fib.unique,genes.deg.SM.unique,genes.deg.Endo.unique,genes.deg.Leu.unique),g=c("Fib","SM","Endo","Leu"))
sc10x.D17 <- scSubset(sc10x,i="samples",g=c("D17PrPzF_BE","D17PrPzF_LE","D17PrPzF_OE","D17PrPzF_FMSt","D17PrPzF_Via","D17PrTzF_Via"))
sc10x.D17.Epi <- scSubset(sc10x.Epi,i="samples",g=c("D17PrPzF_BE","D17PrPzF_LE","D17PrPzF_OE","D17PrPzF_FMSt","D17PrPzF_Via","D17PrTzF_Via"))
sc10x.D17.Epi.NE <- scSubset(sc10x.Epi.NE,i="samples",g=c("D17PrPzF_BE","D17PrPzF_LE","D17PrPzF_OE","D17PrPzF_FMSt","D17PrPzF_Via","D17PrTzF_Via"))
sc10x.D17.St <- scSubset(sc10x.St,i="samples",g=c("D17PrPzF_BE","D17PrPzF_LE","D17PrPzF_OE","D17PrPzF_FMSt","D17PrPzF_Via","D17PrTzF_Via"))
sc10x.D17 <- RunTSNE(object=sc10x.D17,dims.use=1:pc.use.poststress,do.fast=TRUE)
sc10x.D17.Epi <- RunTSNE(object=sc10x.D17.Epi,dims.use=1:pc.use.poststress,do.fast=TRUE)
sc10x.D17.Epi.NE <- RunTSNE(object=sc10x.D17.Epi.NE,dims.use=1:pc.use.poststress,do.fast=TRUE)
sc10x.D17.St <- RunTSNE(object=sc10x.D17.St,dims.use=1:pc.use.poststress,do.fast=TRUE)
sctSNECustCol(sc10x.D17,i="Lin",bl="Epi",rd="St",file="D17")
sctSNECustCol(sc10x.D17,i="Merge_Epi.dws.sc_St.dws.sc",bl=c("BE","LE","OE_SCGB","OE_KRT13"),rd=c("Fib","SM","Endo","Leu"),file="D17")
sctSNECustCol(sc10x.D17.Epi,i="Epi.dws.sc",bl=c("BE","LE","OE_SCGB","OE_KRT13"),rd="",file="D17.Epi")
sctSNECustCol(sc10x.D17.St,i="St.dws.sc",bl="",rd=c("Fib","SM","Endo","Leu"),file="D17.St")
sctSNEbwCol(sc10x.D17,i="res0.2",file="ALL",files="D17")
sctSNEbwCol(sc10x.D17.Epi,i="res0.2",file="Epi",files="D17")
sctSNEbwCol(sc10x.D17.St,i="res0.2",file="St",files="D17")
sctSNEbwCol(sc10x.D17,i="Merge_Epi.dws.sc_St.dws.sc",file="ALL",files="D17")
sctSNEbwCol(sc10x.D17.Epi,i="Epi.dws.sc",file="Epi",files="D17")
sctSNEbwCol(sc10x.D17.St,i="St.dws.sc",file="St",files="D17")
for (g in c("Epi","St")){
sctSNEHighlight(sc10x.D17,i="Lin",g=g,file="D17")
}
for (g in c("BE","LE","OE_SCGB","OE_KRT13")){
sctSNEHighlight(sc10x.D17,i="Merge_Epi.dws.sc_St.dws.sc",g=g,file="D17")
sctSNEHighlight(sc10x.D17.Epi,i="Epi.dws.sc",g=g,file="D17")
}
sctSNEHighlight(sc10x.D17.Epi.NE,i="NE",g="NE",file="D17")
for (g in c("Fib","SM","Endo","Leu")){
sctSNEHighlight(sc10x.D17,i="Merge_Epi.dws.sc_St.dws.sc",g=g,file="D17")
sctSNEHighlight(sc10x.D17.St,i="St.dws.sc",g=g,file="D17")
}
for (g in c("D17PrPzF_BE","D17PrPzF_LE","D17PrPzF_OE","D17PrPzF_FMSt","D17PrPzF_Via","D17PrTzF_Via")){
sctSNEHighlight(sc10x.D17,i="samples",g=g,file="D17")
}
rm(g)
sc10x.D27 <- scSubset(sc10x,i="samples",g=c("D27PrTzF_BE","D27PrTzF_LE","D27PrTzF_OE","D27PrTzF_Edn","D27PrTzF_StPDPNp","D27PrTzF_StPDPNn","D27PrPzF_Via","D27PrTzF_Via"))
sc10x.D27.Epi <- scSubset(sc10x.Epi,i="samples",g=c("D27PrTzF_BE","D27PrTzF_LE","D27PrTzF_OE","D27PrTzF_Edn","D27PrTzF_StPDPNp","D27PrTzF_StPDPNn","D27PrPzF_Via","D27PrTzF_Via"))
sc10x.D27.Epi.NE <- scSubset(sc10x.Epi.NE,i="samples",g=c("D27PrTzF_BE","D27PrTzF_LE","D27PrTzF_OE","D27PrTzF_Edn","D27PrTzF_StPDPNp","D27PrTzF_StPDPNn","D27PrPzF_Via","D27PrTzF_Via"))
sc10x.D27.St <- scSubset(sc10x.St,i="samples",g=c("D27PrTzF_BE","D27PrTzF_LE","D27PrTzF_OE","D27PrTzF_Edn","D27PrTzF_StPDPNp","D27PrTzF_StPDPNn","D27PrPzF_Via","D27PrTzF_Via"))
sc10x.D27 <- RunTSNE(object=sc10x.D27,dims.use=1:pc.use.poststress,do.fast=TRUE)
sc10x.D27.Epi <- RunTSNE(object=sc10x.D27.Epi,dims.use=1:pc.use.poststress,do.fast=TRUE)
sc10x.D27.Epi.NE <- RunTSNE(object=sc10x.D27.Epi.NE,dims.use=1:pc.use.poststress,do.fast=TRUE)
sc10x.D27.St <- RunTSNE(object=sc10x.D27.St,dims.use=1:pc.use.poststress,do.fast=TRUE)
sctSNECustCol(sc10x.D27,i="Lin",bl="Epi",rd="St",file="D27")
sctSNECustCol(sc10x.D27,i="Merge_Epi.dws.sc_St.dws.sc",bl=c("BE","LE","OE_SCGB","OE_KRT13"),rd=c("Fib","SM","Endo","Leu"),file="D27")
sctSNECustCol(sc10x.D27.Epi,i="Epi.dws.sc",bl=c("BE","LE","OE_SCGB","OE_KRT13"),rd="",file="D27.Epi")
sctSNECustCol(sc10x.D27.St,i="St.dws.sc",bl="",rd=c("Fib","SM","Endo","Leu"),file="D27.St")
sctSNEbwCol(sc10x.D27,i="res0.2",file="ALL",files="D27")
sctSNEbwCol(sc10x.D27.Epi,i="res0.2",file="Epi",files="D27")
sctSNEbwCol(sc10x.D27.St,i="res0.2",file="St",files="D27")
sctSNEbwCol(sc10x.D27,i="Merge_Epi.dws.sc_St.dws.sc",file="ALL",files="D27")
sctSNEbwCol(sc10x.D27.Epi,i="Epi.dws.sc",file="Epi",files="D27")
sctSNEbwCol(sc10x.D27.St,i="St.dws.sc",file="St",files="D27")
for (g in c("Epi","St")){
sctSNEHighlight(sc10x.D27,i="Lin",g=g,file="D27")
}
for (g in c("BE","LE","OE_SCGB","OE_KRT13")){
sctSNEHighlight(sc10x.D27,i="Merge_Epi.dws.sc_St.dws.sc",g=g,file="D27")
sctSNEHighlight(sc10x.D27.Epi,i="Epi.dws.sc",g=g,file="D27")
}
sctSNEHighlight(sc10x.D27.Epi.NE,i="NE",g="NE",file="D27")
for (g in c("Fib","SM","Endo","Leu")){
sctSNEHighlight(sc10x.D27,i="Merge_Epi.dws.sc_St.dws.sc",g=g,file="D27")
sctSNEHighlight(sc10x.D27.St,i="St.dws.sc",g=g,file="D27")
}
for (g in c("D27PrTzF_BE","D27PrTzF_LE","D27PrTzF_OE","D27PrTzF_Edn","D27PrTzF_StPDPNp","D27PrTzF_StPDPNn","D27PrPzF_Via","D27PrTzF_Via")){
sctSNEHighlight(sc10x.D27,i="samples",g=g,file="D27")
}
rm(g)
sc10x.D27 <- SetAllIdent(object=sc10x.D27,id="samples")
cell <- names(sc10x.D27@ident[grep("^D27PrTzF_StPDPN",as.character(sc10x.D27@ident))])
sc10x.D27 <- SetIdent(object=sc10x.D27,cells.use=cell,ident.use="D27PrTzF_FMSt")
rm(cell)
sctSNEHighlight(sc10x.D27,i="current",g="D27PrTzF_FMSt",file="D27")
sc10x <- SetAllIdent(object=sc10x,id="samples")
cell <- names(sc10x@ident[grep("D17PrTzF_Via",as.character(sc10x@ident))])
sc10x <- SetIdent(object=sc10x,cells.use=cell,ident.use="DPrTzF_Via")
cell <- names(sc10x@ident[grep("D27PrTzF_Via",as.character(sc10x@ident))])
sc10x <- SetIdent(object=sc10x,cells.use=cell,ident.use="DPrTzF_Via")
rm(cell)
sctSNEHighlight(sc10x,i="current",g="DPrTzF_Via",file="DPrTzF")
sc10x <- SetAllIdent(object=sc10x,id="samples")
cell <- names(sc10x@ident[grep("D17PrPzF_Via",as.character(sc10x@ident))])
sc10x <- SetIdent(object=sc10x,cells.use=cell,ident.use="DPrPzF_Via")
cell <- names(sc10x@ident[grep("D27PrPzF_Via",as.character(sc10x@ident))])
sc10x <- SetIdent(object=sc10x,cells.use=cell,ident.use="DPrPzF_Via")
rm(cell)
sctSNEHighlight(sc10x,i="current",g="DPrPzF_Via",file="DPrPzF")
sc10x.Via <- scSubset(sc10x,i="samples",g=c("D17PrPzF_Via","D17PrTzF_Via","D27PrPzF_Via","D27PrTzF_Via"))
gene.set.c2.all <- read.gmt("./genesets/c2.all.v6.1.symbols.gmt")
results.cor.c2.ALL <- scQuSAGElg(sc10x.Via,gs=gene.set.c2.all,ds=opt$ds,nm="Merge_Epi.dws.sc_St.dws.sc",folder="c2.all")
save(list=ls(pattern="^sc10x.D17"),file="./analysis/sc10x.D17.Rda")
rm(list=ls(pattern="^sc10x.D17"))
save(list=ls(pattern="^sc10x.D27"),file="./analysis/sc10x.D27.Rda")
rm(list=ls(pattern="^sc10x.D27"))
save(list=ls(pattern="sc10x.Via"),file="./analysis/sc10x.Via.Rda")
rm(list=ls(pattern="sc10x.Via"))
\ No newline at end of file
r.scripts/sc-TissueMapper_RUN.D.pseudotime.R deleted 100644 → 0
+ 0
− 16
View file @ 80d84d6b
gc()
library(methods)
library(Seurat)
library(monocle)
library(dplyr)
setwd("../")
source("./r.scripts/sc-TissueMapper.R")
load("./analysis/sc10x.Epi.Rda")
if (!dir.exists("./analysis/pseudotime")){
dir.create("./analysis/pseudotime")
}
scPseudotime(sc10x.Epi,i="Epi.dws.sc",ds=10000)
r.scripts/sc-TissueMapper_RUN.D17.R deleted 100644 → 0
+ 0
− 396
View file @ 80d84d6b
gc()
library(methods)
library(optparse)
library(Seurat)
library(readr)
library(fBasics)
library(pastecs)
library(qusage)
library(RColorBrewer)
source("../r.scripts/sc-TissueMapper.R")
#Create folder structure
setwd("../")
if (!dir.exists("./analysis")){
dir.create("./analysis")
}
if (!dir.exists("./analysis/qc")){
dir.create("./analysis/qc")
}
if (!dir.exists("./analysis/qc/cc")){
dir.create("./analysis/qc/cc")
}
if (!dir.exists("./analysis/tSNE")){
dir.create("./analysis/tSNE")
}
if (!dir.exists("./analysis/tSNE/pre.stress")){
dir.create("./analysis/tSNE/pre.stress")
}
if (!dir.exists("./analysis/pca")){
dir.create("./analysis/pca")
}
if (!dir.exists("./analysis/pca/stress")){
dir.create("./analysis/pca/stress")
}
if (!dir.exists("./analysis/violin")){
dir.create("./analysis/violin")
}
if (!dir.exists("./analysis/violin/stress")){
dir.create("./analysis/violin/stress")
}
if (!dir.exists("./analysis/table")){
dir.create("./analysis/table")
}
if (!dir.exists("./analysis/tSNE/post.stress")){
dir.create("./analysis/tSNE/post.stress")
}
if (!dir.exists("./analysis/cor")){
dir.create("./analysis/cor")
}
if (!dir.exists("./analysis/tSNE/lin")){
dir.create("./analysis/tSNE/lin")
}
if (!dir.exists("./analysis/tSNE/epi")){
dir.create("./analysis/tSNE/epi")
}
if (!dir.exists("./analysis/tSNE/st")){
dir.create("./analysis/tSNE/st")
}
if (!dir.exists("./analysis/tSNE/merge")){
dir.create("./analysis/tSNE/merge")
}
if (!dir.exists("./analysis/pca/ne")){
dir.create("./analysis/pca/ne")
}
if (!dir.exists("./analysis/tSNE/ne")){
dir.create("./analysis/tSNE/ne")
}
if (!dir.exists("./analysis/violin/ne")){
dir.create("./analysis/violin/ne")
}
if (!dir.exists("./analysis/tSNE/FINAL")){
dir.create("./analysis/tSNE/FINAL")
}
if (!dir.exists("./analysis/deg")){
dir.create("./analysis/deg")
}
if (!dir.exists("./analysis/diy")){
dir.create("./analysis/diy")
}
#Retrieve command-line options
option_list=list(
make_option("--p",action="store",default="D17PrF",type='character',help="Project Name"),
make_option("--g",action="store",default="ALL",type='character',help="Group To analyze"),
make_option("--lg",action="store",default=500,type='integer',help="Threshold for cells with minimum genes"),
make_option("--hg",action="store",default=2500,type='integer',help="Threshold for cells with maximum genes"),
make_option("--lm",action="store",default=0,type='numeric',help="Threshold for cells with minimum %mito genes"),
make_option("--hm",action="store",default=0.1,type='numeric',help="Threshold for cells with maximum %mito genes"),
make_option("--lx",action="store",default=0.0125,type='numeric',help="x low threshold for hvg selection"),
make_option("--hx",action="store",default=3.5,type='numeric',help="x high threshold for hvg selection"),
make_option("--ly",action="store",default=0.5,type='numeric',help="y low threshold for hvg selection"),
make_option("--cc",action="store",default=TRUE,type='logical',help="Scale cell cycle?"),
make_option("--pc",action="store",default=25,type='integer',help="Number of PCs to cacluate"),
make_option("--hpc",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, pre-stress"),
make_option("--res.prestress",action="store",default=1,type='numeric',help="Resolution to cluster, pre-stress"),
make_option("--st",action="store",default="TRUE",type='logical',help="Remove stressed cells?"),
make_option("--stg",action="store",default="go",type='character',help="Geneset to use for stress ID"),
#make_option("--hpc.poststress",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
make_option("--res.poststress",action="store",default=0.2,type='numeric',help="Resolution to cluster, post-stress"),
make_option("--ds",action="store",default=50000,type='integer',help="Number of cells to downsample"),
#make_option("--hpc.epi",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, Epi"),
make_option("--res.epi",action="store",default=0.2,type='numeric',help="Resolution to cluster, Epi"),
#make_option("--hpc.st",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, St"),
make_option("--res.st",action="store",default=0.3,type='numeric',help="Resolution to cluster, St")
)
opt=parse_args(OptionParser(option_list=option_list))
rm(option_list)
if (opt$lm==0){opt$lm=-Inf}
sc10x <- scLoad(opt$p,sub=TRUE)
sc10x <- scSubset(sc10x,"ALL",opt$g)
if (opt$cc==TRUE){
results <- scCellCycle(sc10x)
sc10x <- results[[1]]
genes.s <- results[[2]]
genes.g2m <- results[[3]]
rm(results)
} else {
genes.s=""
genes.g2m=""
}
results <- scQC(sc10x,lg=opt$lg,hg=opt$hg,lm=opt$lm,hm=opt$hm)
sc10x <- results[[1]]
counts.cell.raw <- results[[2]]
counts.gene.raw <- results[[3]]
counts.cell.filtered <- results[[4]]
counts.gene.filtered <- results[[5]]
rm(results)
results <- scPC(sc10x,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=opt$pc,hpc=opt$hpc,file="pre.stress")
sc10x <- results[[1]]
genes.hvg.prestress <- results[[2]]
pc.use.prestress <- results[[3]]
rm(results)
sc10x <- scCluster(sc10x,pc.use=pc.use.prestress,res.use=opt$res.prestress,folder="pre.stress")
if (opt$st==TRUE){
results <- scStress(sc10x,stg=opt$stg,res.use=opt$res.prestress,pc.use=pc.use.prestress,cut=0.9)
sc10x <- results[[1]]
counts.cell.filtered.stress <- results[[2]]
sc10x.Stress <- results[[3]]
rm(results)
results <- scPC(sc10x,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=opt$pc,hpc=opt$hpc,file="post.stress")
sc10x <- results[[1]]
genes.hvg.poststress <- results[[2]]
pc.use.poststress <- results[[3]]
rm(results)
sc10x <- scCluster(sc10x,pc.use=pc.use.poststress,res.use=opt$res.poststress,folder="post.stress")
}
gene.set1 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "St"
gene.set <- c(gene.set1)
gene.set1 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "Epi"
gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=opt$ds,nm="Lin",folder="lin")
sc10x <- results[[1]]
results.cor.Lin <- results[[2]]
results.clust.Lin.id <- results[[3]]
rm(results)
rm(gene.set)
sc10x.Epi <- scSubset(sc10x,i="Lin",g="Epi")
if (any(levels(sc10x@ident)=="Unknown")){
sc10x.St <- scSubset(sc10x,i="Lin",g=c("St","Unknown"))
} else {
sc10x.St <- scSubset(sc10x,i="Lin",g="St")
}
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=opt$res.epi,folder="epi")
gene.set1 <- read_delim("./genesets/DEG_BE_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "BE"
gene.set <- c(gene.set1)
gene.set1 <- read_delim("./genesets/DEG_LE_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "LE"
gene.set <- c(gene.set,gene.set1)
gene.set1 <- read_delim("./genesets/DEG_OE_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "OE"
gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
results <- scQuSAGE(sc10x.Epi,gs=gene.set,res.use=opt$res.epi,ds=opt$ds,nm="Epi.dws",folder="epi")
sc10x.Epi <- results[[1]]
results.cor.Epi.dws <- results[[2]]
results.clust.Epi.dws.id <- results[[3]]
rm(results)
rm(gene.set)
sc10x.Epi <- SetAllIdent(object=sc10x.Epi,id=paste0("res",opt$res.epi))
OE <- levels(factor(sc10x.Epi@ident[sc10x.Epi@meta.data$Epi.dws=="OE"]))
OE.cells <- NULL
for (i in 1:length(OE)){
OE.cells[i] <- list(names(sc10x.Epi@ident[sc10x.Epi@ident==OE[i]]))
}
sc10x.Epi <- SetAllIdent(object=sc10x.Epi,id="Epi.dws")
for (i in 1:length(OE)){
sc10x.Epi <- SetIdent(object=sc10x.Epi,cells.use=unlist(OE.cells[i]),ident.use=paste0("OE",i))
}
sc10x.Epi <- StashIdent(object=sc10x.Epi,save.name="Epi.dws.sub")
postscript("./analysis/tSNE/epi/tSNE_Epi.dws.sub.eps")
plot <- TSNEPlot(object=sc10x.Epi,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))
plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
plot(plot)
dev.off()
rm(plot)
rm(OE)
rm(OE.cells)
sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=opt$res.st,folder="st")
gene.set1 <- read_delim("./genesets/DEG_C5.BP.M11704.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set1 <- as.list(gene.set1[-1,])
names(gene.set1) <- "Endo"
gene.set <- c(gene.set1)
gene.set1 <- read_delim("./genesets/DEG_C5.BP.M10794.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set1 <- as.list(gene.set1[-1,])
names(gene.set1) <- "SM"
gene.set <- c(gene.set,gene.set1)
gene.set1 <- read_delim("./genesets/DEG_C5.BP.M13024.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set1 <- as.list(gene.set1[-1,])
names(gene.set1) <- "Fib"
gene.set <- c(gene.set,gene.set1)
gene.set1 <- read_delim("./genesets/DEG_C5.BP.M10124.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set1 <- as.list(gene.set1[-1,])
names(gene.set1) <- "Leu"
gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=opt$res.st,ds=opt$ds,nm="St.go",folder="st")
sc10x.St <- results[[1]]
results.cor.St.go <- results[[2]]
results.clust.St.go.id <- results[[3]]
rm(results)
rm(gene.set)
sc10x.Epi.NE <- scNE(sc10x.Epi,neg="EurUro",cut=0.999)
sc10x.Epi <- scMergeSubClust(sc10x.Epi,i="Epi.dws.sub",g=c("BE","LE"),nm="Merge")
sc10x.St <- scMergeSubClust(sc10x.St,i="St.go",g=c("Endo","SM","Fib","Leu"),nm="Merge")
sc10x <- scMerge(sc10x,sc10x.Epi,sc10x.St,i.1="Merge",i.2="Merge",nm="Merge_Epi.dws_St.go")
sc10x <- scMerge(sc10x,sc10x,sc10x.Epi.NE,i.1="Merge_Epi.dws_St.go",i.2="NE",nm="Merge_Epi.dws_St.go_NE")
sc10x <- SetAllIdent(object=sc10x,id="Merge_Epi.dws_St.go")
sc10x@ident <- factor(sc10x@ident,levels=c("BE","LE","OE1","OE2","Fib","SM","Endo","Leu"))
postscript("./analysis/tSNE/FINAL/tSNE_FINAL.eps")
plot <- TSNEPlot(object=sc10x,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))
plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
plot(plot)
dev.off()
scTables(sc10x,i.1="samples",i.2="Merge_Epi.dws_St.go")
scTables(sc10x,i.1="samples",i.2="Merge_Epi.dws_St.go_NE")
scTables(sc10x,i.1="Merge_Epi.dws_St.go_NE",i.2="Merge_Epi.dws_St.go")
genes.deg.Stress <- scDEG(sc10x.Stress,i="Stress",g.1="Stress",g.2="ALL",pct=0.5,t=5)
genes.deg.Epi <- scDEG(sc10x,i="Lin",g.1="Epi",g.2="St",t=2)
genes.deg.St <- scDEG(sc10x,i="Lin",g.1="St",g.2="Epi",t=2)
genes.deg.BE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="BE",g.2=c("LE","OE1","OE2"),pct=0.25,t=2)
genes.deg.LE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="LE",g.2=c("BE","LE","OE1"),pct=0.25,t=2)
genes.deg.OE1 <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="OE1",g.2=c("BE","LE","OE2"),pct=0.25,t=2)
genes.deg.OE2 <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="OE2",g.2=c("BE","LE","OE1"),pct=0.25,t=2)
genes.deg.NE <- scDEG(sc10x.Epi.NE,i="NE",g.1="NE",g.2="ALL",pct=0.01,t=1)
genes.deg.Fib <- scDEG(sc10x.St,i="Merge_Epi.dws_St.go_NE",g.1="Fib",g.2=c("SM","Endo","Leu"),pct=0.25,t=2)
genes.deg.SM <- scDEG(sc10x.St,i="Merge_Epi.dws_St.go_NE",g.1="SM",g.2=c("Fib","Endo","Leu"),pct=0.25,t=2)
genes.deg.Endo <- scDEG(sc10x.St,i="Merge_Epi.dws_St.go_NE",g.1="Endo",g.2=c("Fib","SM","Leu"),pct=0.25,t=2)
genes.deg.Leu <- scDEG(sc10x.St,i="St.go",g.1="Leu",g.2=c("Fib","SM","Endo"),pct=0.25,t=2)
genes.deg.BE.unique <- setdiff(rownames(genes.deg.BE),Reduce(union,list(rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.LE.unique <- setdiff(rownames(genes.deg.LE),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.OE1.unique <- setdiff(rownames(genes.deg.OE1),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.OE2.unique <- setdiff(rownames(genes.deg.OE2),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.NE.unique <- setdiff(rownames(genes.deg.NE),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.Fib.unique <- setdiff(rownames(genes.deg.Fib),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.SM.unique <- setdiff(rownames(genes.deg.SM),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.Endo.unique <- setdiff(rownames(genes.deg.Endo),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Leu))))
genes.deg.Leu.unique <- setdiff(rownames(genes.deg.Leu),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo))))
genes.deg.5 <- c(genes.deg.BE.unique[1:5],genes.deg.LE.unique[1:5],genes.deg.OE1.unique[1:5],genes.deg.OE2.unique[1:5],genes.deg.NE.unique[1:5],genes.deg.Fib.unique[1:5],genes.deg.SM.unique[1:5],genes.deg.Endo.unique[1:5],genes.deg.Leu.unique[1:5])
genes.deg.5 <- rev(genes.deg.5)
genes.deg.10 <- c(genes.deg.BE.unique[1:10],genes.deg.LE.unique[1:10],genes.deg.OE1.unique[1:10],genes.deg.OE2.unique[1:10],genes.deg.NE.unique[1:10],genes.deg.Fib.unique[1:10],genes.deg.SM.unique[1:10],genes.deg.Endo.unique[1:10],genes.deg.Leu.unique[1:10])
genes.deg.10 <- rev(genes.deg.10)
sc10x <- SetAllIdent(object=sc10x,id="Merge_Epi.dws_St.go_NE")
sc10x <- SetAllIdent(object=sc10x,id="Merge_Epi.dws_St.go_NE")
sc10x@ident <- factor(sc10x@ident,levels=c("BE","LE","OE1","OE2","NE","Fib","SM","Endo","Leu"))
postscript("./analysis/deg/Dot.DEG.eps",paper="special",width=10,height=5,horizontal=FALSE)
DotPlot(sc10x,genes.deg.5,x.lab.rot=TRUE,plot.legend=TRUE,dot.scale=4)
dev.off()
postscript("./analysis/deg/Heatmap.DEG.eps",paper="special",width=10,height=5,horizontal=FALSE)
plot(DoHeatmap(sc10x,genes.use=genes.deg.10,slim.col.label=TRUE,group.label.rot=TRUE,group.spacing=0.25,cex.row=2.5))
dev.off()
for (i in ls(pattern="^genes.deg*unique")){
postscript(paste0("./analysis/deg/Violin.",i,".eps"),paper="special",width=10,height=5,horizontal=FALSE)
plot(VlnPlot(sc10x,features.plot=get(i)[1:10],nCol=5,point.size.use=0.1,size.title.use=15,x.lab.rot=TRUE))
dev.off()
postscript(paste0("./analysis/deg/Ridge.",i,".eps"),paper="special",width=10,height=5,horizontal=FALSE)
plot(RidgePlot(sc10x,features.plot=get(i)[1:10],nCol=5,size.x.use=10,size.title.use=15))
dev.off()
postscript(paste0("./analysis/deg/Heatmap.",i,".eps"),paper="special",width=10,height=5,horizontal=FALSE)
plot(DoHeatmap(sc10x,genes.use=get(i),slim.col.label=TRUE,group.label.rot=TRUE,group.spacing=0.25,cex.row=2.5))
dev.off()
}
sc10x.Stress <- SetAllIdent(object=sc10x.Stress,id="Stress")
postscript("./analysis/deg/Violin.Stress.eps",paper="special",width=10,height=5,horizontal=FALSE)
plot(VlnPlot(sc10x.Stress,features.plot=rownames(genes.deg.Stress)[1:10],nCol=5,point.size.use=0.1,size.title.use=15,x.lab.rot=TRUE))
dev.off()
postscript("./analysis/deg/Ridge.Stress.eps",paper="special",width=10,height=5,horizontal=FALSE)
plot(RidgePlot(sc10x.Stress,features.plot=rownames(genes.deg.Stress)[1:10],nCol=5,size.x.use=10,size.title.use=15))
dev.off()
postscript("./analysis/deg/Heatmap.Stress.eps",paper="special",width=10,height=5,horizontal=FALSE)
plot(DoHeatmap(sc10x.Stress,genes.use=rownames(genes.deg.Stress),slim.col.label=TRUE,group.label.rot=TRUE,group.spacing=0.25,cex.row=2.5))
dev.off()
sc10x.Epi.NE <- SetAllIdent(object=sc10x.Epi.NE,id="NE")
postscript("./analysis/deg/Violin.NE.eps",paper="special",width=10,height=5,horizontal=FALSE)
plot(VlnPlot(sc10x.Epi.NE,features.plot=rownames(genes.deg.NE)[1:10],nCol=5,point.size.use=0.1,size.title.use=15,x.lab.rot=TRUE))
dev.off()
postscript("./analysis/deg/Ridge.NE.eps",paper="special",width=10,height=5,horizontal=FALSE)
plot(RidgePlot(sc10x.Epi.NE,features.plot=rownames(genes.deg.NE)[1:10],nCol=5,size.x.use=10,size.title.use=15))
dev.off()
for (i in ls(pattern="^genes.deg")){
write.table(get(i),file=paste0("./analysis/deg/",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
}
sctSNECustCol(sc10x,i="Lin",bl="Epi",rd="St",file="D17")
sctSNECustCol(sc10x,i="Merge_Epi.dws_St.go",bl=c("BE","LE","OE1","OE2"),rd=c("Fib","SM","Endo","Leu"),file="D17")
sctSNECustCol(sc10x.Epi,i="Epi.dws.sub",bl=c("BE","LE","OE1","OE2"),rd="",file="D17")
sctSNECustCol(sc10x.St,i="St.go",bl="",rd=c("Fib","SM","Endo","Leu"),file="D17")
sctSNEbwCol(sc10x,i="res0.2",file="ALL",files="D17")
sctSNEbwCol(sc10x.Epi,i="res0.2",file="Epi",files="D17")
sctSNEbwCol(sc10x.St,i="res0.2",file="St",files="D17")
sctSNEbwCol(sc10x,i="Merge_Epi.dws_St.go",file="ALL",files="D17")
sctSNEbwCol(sc10x.Epi,i="Epi.dws.sub",file="Epi",files="D17")
sctSNEbwCol(sc10x.St,i="St.go",file="St",files="D17")
for (g in c("Epi","St")){
sctSNEHighlight(sc10x,i="Lin",g=g,file="D17")
}
for (g in c("BE","LE","OE1","OE2")){
sctSNEHighlight(sc10x,i="Merge_Epi.dws_St.go",g=g,file="D17")
sctSNEHighlight(sc10x.Epi,i="Epi.dws.sub",g=g,file="D17")
}
sctSNEHighlight(sc10x.Epi.NE,i="NE",g="NE",file="D17")
for (g in c("Fib","SM","Endo","Leu")){
sctSNEHighlight(sc10x,i="Merge_Epi.dws_St.go",g=g,file="D17")
sctSNEHighlight(sc10x.St,i="St.go",g=g,file="D17")
}
for (g in c("D17PrPzF_BE","D17PrPzF_LE","D17PrPzF_OE","D17PrPzF_FMSt","D17PrPzF_Via","D17PrTzF_Via")){
sctSNEHighlight(sc10x,i="samples",g=g,file="D17")
}
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"))
save(list=ls(pattern="sc10x.Stress"),file="./analysis/sc10x.Stress.Rda")
rm(list=ls(pattern="sc10x.Stress"))
save(list=ls(pattern="^genes.deg"),file="./analysis/DEG.Rda")
rm(list=ls(pattern="^genes.deg"))
save(list=ls(pattern="sc10x.Epi"),file="./analysis/sc10x.Epi.Rda")
rm(list=ls(pattern="^sc10x.Epi"))
save(list=ls(pattern="sc10x.St"),file="./analysis/sc10x.St.Rda")
rm(list=ls(pattern="sc10x.St"))
save(list=ls(pattern="^sc10x"),file="./analysis/sc10x.Rda")
rm(list=ls(pattern="^sc10x"))
save.image(file="./analysis/Data.RData")
r.scripts/sc-TissueMapper_RUN.D2.R deleted 100644 → 0
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