Add diy for DPrF including D17 and D27 isolated figures

r.scripts/sc-TissueMapper_RUN.D.diy.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"))
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