Set SingleR project name by cli

bash.scripts/sc10x.id.sh

@@ -14,4 +14,4 @@ source activate umap
 module load R/3.5.1-gccmkl
 module load hdf5_18/1.8.17
 
-Rscript ../r.scripts/SingleR.R
+Rscript ../r.scripts/SingleR.R --p "$1" --s "$2"

r.scripts/SingleR.R

@@ -36,7 +36,7 @@ load("./analysis/sc10x.raw.RData")
 load("./genesets/scDWS.250.rda")
 load("./genesets/cibersort.rda")
 
-singler = CreateBigSingleRObject(GetAssayData(sc10x,assay="SCT"), annot = NULL, "PdPbPc", min.genes = 0,
+singler = CreateBigSingleRObject(GetAssayData(sc10x,assay="SCT"), annot = NULL, opt$p, min.genes = 0,
                               technology = "10X", species = "Human", citation = "",
                               ref.list = list(scDWS.250), normalize.gene.length = F, variable.genes = "de",
                               fine.tune = T, do.signatures = T, clusters = NULL, do.main.types = F, 
@@ -129,7 +129,7 @@ for (i in c("epi","fmst","st","leu")){
   dev.off()
 }
 
-singler.leu = CreateSinglerObject(GetAssayData(sc10x.leu,assay="SCT"), annot = NULL, "PdPbPc", min.genes = 0,
+singler.leu = CreateSinglerObject(GetAssayData(sc10x.leu,assay="SCT"), annot = NULL, opt$p, min.genes = 0,
                               technology = "10X", species = "Human", citation = "",
                               ref.list = list(cibersort), normalize.gene.length = F, variable.genes = "de",
                               fine.tune = T, do.signatures = T, clusters = NULL, do.main.types = T,