From 0edebb0aa2cf7cd49271055e7f1484d2c134ca1b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 8 Aug 2018 16:25:57 -0500
Subject: [PATCH] Change CCA: calculate 25, align 15
---
r.scripts/sc-TissueMapper.R | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/r.scripts/sc-TissueMapper.R b/r.scripts/sc-TissueMapper.R
index 702ab55..ecc5c2b 100644
--- a/r.scripts/sc-TissueMapper.R
+++ b/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)
--
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