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| author | Alexander Kabui | 2021-10-05 15:14:25 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-10-25 14:16:21 +0300 |
| commit | 453570cbf22a92de72fa0401895c99a923831942 (patch) | |
| tree | 62b18442540b372ab70ea5d157127365d6b56a1e | |
| parent | 838276a6c4effc6985a888a32d148ef8942b526a (diff) | |
| download | genenetwork3-453570cbf22a92de72fa0401895c99a923831942.tar.gz | |
script modification : add debug statements
| -rw-r--r-- | scripts/wgcna_analysis.R | 16 |
1 files changed, 15 insertions, 1 deletions
diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R index 17b3537..a5cbbe3 100644 --- a/scripts/wgcna_analysis.R +++ b/scripts/wgcna_analysis.R @@ -6,11 +6,15 @@ 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 +25,7 @@ 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 +88,11 @@ 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="_") @@ -95,6 +105,10 @@ 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, |