Fix R data file saves

r.scripts/sc-TissueMapper_RUN.D.R

@@ -374,8 +374,14 @@ 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=",")
 }
 
+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.D17.R

@@ -390,12 +390,14 @@ 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")
+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.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.D27.R

@@ -275,6 +275,14 @@ scTables(sc10x,i.1="samples",i.2="Merge_Epi.dws.sc_St.dws.sc")
 scTables(sc10x,i.1="samples",i.2="Merge_Epi.dws.sc_St.dws.sc_NE")
 scTables(sc10x,i.1="Merge_Epi.dws.sc_St.dws.sc_NE",i.2="Merge_Epi.dws.sc_St.dws.sc")
 
+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")