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| author | Frederick Muriuki Muriithi | 2021-10-25 15:13:05 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2021-10-25 15:13:05 +0300 |
| commit | 5a472ebab04c68cd5228f253cc98d0ae22a520d7 (patch) | |
| tree | 3d6b1a5a8933896a6e7fdc98f473ef069accd348 /scripts | |
| parent | 0814eea6b57e45d4337424e63c164d204d03b64d (diff) | |
| parent | 5440bfcd6940db08c4479a39ba66dbc802b2c426 (diff) | |
| download | genenetwork3-5a472ebab04c68cd5228f253cc98d0ae22a520d7.tar.gz | |
Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-correlations
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/wgcna_analysis.R | 17 |
1 files changed, 15 insertions, 2 deletions
diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R index 17b3537..b0d25a9 100644 --- a/scripts/wgcna_analysis.R +++ b/scripts/wgcna_analysis.R @@ -6,11 +6,13 @@ library(rjson) options(stringsAsFactors = FALSE); -imgDir = Sys.getenv("GENERATED_IMAGE_DIR") +cat("Running the wgcna analysis script\n") + # load expression data **assumes from json files row(traits)(columns info+samples) # pass the file_path as arg # pass the file path to read json data + args = commandArgs(trailingOnly=TRUE) if (length(args)==0) { @@ -21,6 +23,7 @@ if (length(args)==0) { } inputData <- fromJSON(file = json_file_path) +imgDir = inputData$TMPDIR trait_sample_data <- do.call(rbind, inputData$trait_sample_data) @@ -83,6 +86,11 @@ network <- blockwiseModules(dataExpr, +cat("Generated network \n") + +network + + genImageRandStr <- function(prefix){ randStr <- paste(prefix,stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_") @@ -90,14 +98,19 @@ genImageRandStr <- function(prefix){ return(paste(randStr,".png",sep="")) } + mergedColors <- labels2colors(network$colors) imageLoc <- file.path(imgDir,genImageRandStr("WGCNAoutput")) png(imageLoc,width=1000,height=600,type='cairo-png') + +cat("Generating the CLuster dendrogram\n") + + plotDendroAndColors(network$dendrograms[[1]],mergedColors[network$blockGenes[[1]]], "Module colors", -dendroLabels = FALSE, hang = 0.03, +dendroLabels = NULL, hang = 0.03, addGuide = TRUE, guideHang = 0.05) |