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| author | zsloan | 2021-11-11 11:23:39 -0600 |
|---|---|---|
| committer | GitHub | 2021-11-11 11:23:39 -0600 |
| commit | 8c77af63efae6f06d7c7c3269fc0e41811a8037a (patch) | |
| tree | 9ffa4b84fd36f09e772db3e218bc980999324c41 /scripts/wgcna_analysis.R | |
| parent | 607c6e627c23c1bce3b199b145855182ab51b211 (diff) | |
| parent | 249b85102063debfeeb1b0565956059b8a3af1cf (diff) | |
| download | genenetwork3-8c77af63efae6f06d7c7c3269fc0e41811a8037a.tar.gz | |
Merge branch 'main' into feature/add_rqtl_pairscan
Diffstat (limited to 'scripts/wgcna_analysis.R')
| -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) |