diff options
| -rw-r--r-- | scripts/wgcna_analysis.R | 16 |
1 files changed, 8 insertions, 8 deletions
diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R index 86ddffb..ee749e9 100644 --- a/scripts/wgcna_analysis.R +++ b/scripts/wgcna_analysis.R @@ -20,19 +20,19 @@ if (length(args)==0) { json_file_path = args[1] } -results <- fromJSON(file = json_file_path) +inputData <- fromJSON(file = json_file_path) # parse the json data input -minModuleSize <-results$minModuleSize +minModuleSize <-inputData$minModuleSize -TOMtype <-results$TOMtype +TOMtype <-inputData$TOMtype -corType <-results$corType +corType <-inputData$corType # -trait_sample_data <- do.call(rbind, results$trait_sample_data) +trait_sample_data <- do.call(rbind, inputData$trait_sample_data) dataExpr <- data.frame(apply(trait_sample_data, 2, function(x) as.numeric(as.character(x)))) # transform expressionData @@ -102,12 +102,12 @@ addGuide = TRUE, guideHang = 0.05) -json_data <- list(ModEigens=network$MEs,soft_threshold=sft$fitIndices, +json_data <- list(input = inputData,output = list(ModEigens=network$MEs,soft_threshold=sft$fitIndices, blockGenes =network$blockGenes[[1]], net_colors =network$colors, net_unmerged=network$unmergedColors, - imageLoc=imageLoc) + imageLoc=imageLoc)) json_data <- toJSON(json_data) -write(json_data,"./output.json")
\ No newline at end of file +write(json_data,file= json_file_path)
\ No newline at end of file |