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| author | Alexander Kabui | 2021-09-23 14:22:14 +0300 |
|---|---|---|
| committer | Alexander Kabui | 2021-09-23 14:22:14 +0300 |
| commit | 9216b6ae956b5c78a9b6d21dbd40b6df1e111264 (patch) | |
| tree | 11fb8e7b222a6b65584b58c6afadbb751136d142 /scripts/wgcna_analysis.R | |
| parent | 655343aded3ece533f267bd9fd16aadf0cefff02 (diff) | |
| download | genenetwork3-9216b6ae956b5c78a9b6d21dbd40b6df1e111264.tar.gz | |
validate required output
Diffstat (limited to 'scripts/wgcna_analysis.R')
| -rw-r--r-- | scripts/wgcna_analysis.R | 13 |
1 files changed, 11 insertions, 2 deletions
diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R index 53b59d5..86ddffb 100644 --- a/scripts/wgcna_analysis.R +++ b/scripts/wgcna_analysis.R @@ -14,7 +14,7 @@ imgDir = Sys.getenv("GENERATED_IMAGE_DIR") args = commandArgs(trailingOnly=TRUE) if (length(args)==0) { - stop("Argument for the file location is requires", call.=FALSE) + stop("Argument for the file location is required", call.=FALSE) } else { # default output file json_file_path = args[1] @@ -92,7 +92,6 @@ genImageRandStr <- function(prefix){ mergedColors <- labels2colors(network$colors) imageLoc <- file.path(imgDir,genImageRandStr("WGCNAoutput")) -imageLoc png(imageLoc,width=1000,height=600,type='cairo-png') plotDendroAndColors(network$dendrograms[[1]],mergedColors[network$blockGenes[[1]]], @@ -102,3 +101,13 @@ addGuide = TRUE, guideHang = 0.05) + +json_data <- list(ModEigens=network$MEs,soft_threshold=sft$fitIndices, + blockGenes =network$blockGenes[[1]], + net_colors =network$colors, + net_unmerged=network$unmergedColors, + imageLoc=imageLoc) + +json_data <- toJSON(json_data) + +write(json_data,"./output.json")
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