From 453570cbf22a92de72fa0401895c99a923831942 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 5 Oct 2021 15:14:25 +0300
Subject: script modification : add debug statements

---
 scripts/wgcna_analysis.R | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

(limited to 'scripts')

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,
-- 
cgit v1.2.3


From d1be5270b99959f99802a7704562eeaaeb504122 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 13 Oct 2021 07:29:24 +0300
Subject: minor fixes for sript enable annotations

---
 scripts/wgcna_analysis.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index a5cbbe3..b0d25a9 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -13,8 +13,6 @@ cat("Running the wgcna analysis script\n")
 # pass the file path to read json data
 
 
-
-
 args = commandArgs(trailingOnly=TRUE)
 
 if (length(args)==0) {
@@ -100,6 +98,7 @@ genImageRandStr <- function(prefix){
 	return(paste(randStr,".png",sep=""))
 }
 
+
 mergedColors <- labels2colors(network$colors)
 
 imageLoc <- file.path(imgDir,genImageRandStr("WGCNAoutput"))
@@ -111,7 +110,7 @@ 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)
 
 
-- 
cgit v1.2.3