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-rw-r--r--scripts/wgcna_analysis.R18
1 files changed, 8 insertions, 10 deletions
diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 16a44fd..54650df 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -1,10 +1,14 @@
# initial workspace setup
+
+# todo pass required input data here
library(WGCNA);
library(stringi);
options(stringsAsFactors = FALSE);
+imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
+
# load expression data **assumes csv format row(traits)(columns info+samples)
wgcnaRawData <- read.csv(file = "wgcna_data.csv")
@@ -33,7 +37,7 @@ dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
# network constructions and modules
-# choose softthreshhold (Calculate soft threshold if the user specified the)
+# choose softthreshhold (Calculate soft threshold)
powers <- c(c(1:10), seq(from = 12, to=20, by=2))
sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
@@ -65,12 +69,12 @@ genImageRandStr <- function(prefix){
return(paste(randStr,".png",sep=""))
}
+mergedColors <- labels2colors(net$colors)
-mergedColors = labels2colors(net$colors)
-
-png(genImageRandStr,width=1000,height=600,type='cairo-png')
+imageLoc <- file.path(imgDir,genImageRandStr("WGCNAoutput"))
+png(imageLoc,width=1000,height=600,type='cairo-png')
plotDendroAndColors(network$dendrograms[[1]],mergedColors[net$blockGenes[[1]]],
"Module colors",
@@ -79,9 +83,3 @@ addGuide = TRUE, guideHang = 0.05)
-
-
-
-
-
-