diff --git a/r.scripts/sc-TissueMapper.R b/r.scripts/sc-TissueMapper.R index f8e03ff809b80629f1ee172346ef77da0d9d7ba3..ca0ec8280531dd794e3aabf69877fc2495e80670 100644 --- a/r.scripts/sc-TissueMapper.R +++ b/r.scripts/sc-TissueMapper.R @@ -91,7 +91,7 @@ scCellCycle <- function(sc10x){ genes.s <- genes.cc[1:43] genes.g2m <- genes.cc[44:97] sc10x <- NormalizeData(object=sc10x) - sc10x <- ScaleData(object=sc10x,display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x <- ScaleData(object=sc10x,display.progress=FALSE,do.par=TRUE,num.cores=45) sc10x <- CellCycleScoring(object=sc10x,s.genes=genes.s,g2m.genes=genes.g2m,set.ident=TRUE) postscript("./analysis/qc/cc/Ridge_cc.Raw.eps") @@ -110,7 +110,7 @@ scCellCycle <- function(sc10x){ plot(plot) dev.off() gc() - sc10x <- ScaleData(object=sc10x,vars.to.regress=c("S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x <- ScaleData(object=sc10x,vars.to.regress=c("S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45) gc() sc10x <- RunPCA(object=sc10x,pc.genes=c(genes.s,genes.g2m),do.print=FALSE,pcs.store=2) postscript("./analysis/qc/cc/PCA_cc.Norm.eps") @@ -225,9 +225,9 @@ scPC <- function(sc10x,lx=0.15,hx=3.5,ly=0.75,cc=FALSE,pc=50,hpc=0.75,file="pre. if (cca==FALSE){ gc() if (cc==TRUE){ - sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45) } else { - sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45) } gc() } @@ -982,17 +982,17 @@ scDEG <- function(sc10x,i="Lin",g.1="Epi",g.2="St",pct=0.25,t=2){ scCCA <- function(sc10x.1,sc10x.2,nm.1="D17",nm.2="D27",cc=FALSE){ gc() if (cc==TRUE){ - sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45) } else { - sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45) } gc() gc() if (cc==TRUE){ - sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45) } else { - sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45) } gc() @@ -1052,25 +1052,25 @@ scCCA <- function(sc10x.1,sc10x.2,nm.1="D17",nm.2="D27",cc=FALSE){ sc3CCA <- function(sc10x.1,sc10x.2,sc10x.3,nm.1="D17",nm.2="D27",nm.3="D35",cc=FALSE){ gc() if (cc==TRUE){ - sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45) } else { - sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45) } gc() gc() if (cc==TRUE){ - sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45) } else { - sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45) } gc() gc() if (cc==TRUE){ - sc10x.3 <- ScaleData(object=sc10x.3,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x.3 <- ScaleData(object=sc10x.3,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45) } else { - sc10x.3 <- ScaleData(object=sc10x.3,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=50) + sc10x.3 <- ScaleData(object=sc10x.3,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45) } gc()