Change CCA: calculate 25, align 15

r.scripts/sc-TissueMapper.R

@@ -1006,7 +1006,7 @@ scCCA <-  function(sc10x.1,sc10x.2,nm.1="D17",nm.2="D27",cc=FALSE){
   
   sc10x.1@meta.data$patient <- nm.1
   sc10x.2@meta.data$patient <- nm.2
-  sc10x <- RunCCA(sc10x.1,sc10x.2,genes.use=genes.hvg.Comb,num.cc=50,add.cell.id1=nm.1,add.cell.id2=nm.2)
+  sc10x <- RunCCA(sc10x.1,sc10x.2,genes.use=genes.hvg.Comb,num.cc=25,add.cell.id1=nm.1,add.cell.id2=nm.2)
   rm(sc10x.1)
   rm(sc10x.2)
   
@@ -1026,7 +1026,7 @@ scCCA <-  function(sc10x.1,sc10x.2,nm.1="D17",nm.2="D27",cc=FALSE){
   #dev.off()
   
   gc()
-  sc10x <- AlignSubspace(sc10x,reduction.type="cca",grouping.var="patient",dims.align=1:25)
+  sc10x <- AlignSubspace(sc10x,reduction.type="cca",grouping.var="patient",dims.align=1:15)
   gc()
   
   postscript("./analysis/cca/CCA.Aligned.eps",paper="special",width=10,height=5,horizontal=FALSE)