From 1600992807a0b3edbe10e8c0baf80a41636a7650 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 21:58:20 +0300
Subject: init commit for wgcna script

---
 scripts/wgcna_analysis.R | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 scripts/wgcna_analysis.R

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
new file mode 100644
index 0000000..e69de29
-- 
cgit v1.2.3


From ea0e92d3f63a9f403aacd5ab1590f61f2752158a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 22:12:43 +0300
Subject: load the required data for analysis

---
 scripts/wgcna_analysis.R | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index e69de29..a8170b6 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -0,0 +1,21 @@
+# initial workspace setup
+
+library(WGCNA);
+stringsAsFactors = FALSE
+
+# load expression data **assumes csv format row(traits)(columns info+samples)
+
+
+wgcnaRawData <- read.csv(file = "wgcna_data.csv")
+
+# transform expressionData
+
+datExpr <- as.data.frame(t(wgcnaRawData));
+
+
+
+
+
+
+
+
-- 
cgit v1.2.3


From 49fdd614d4b18f7d28126e4ebbf3adca57f0416f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 22:31:18 +0300
Subject: Checking data for excessive missing values

---
 scripts/wgcna_analysis.R | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index a8170b6..8e90d7d 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -10,10 +10,28 @@ wgcnaRawData <- read.csv(file = "wgcna_data.csv")
 
 # transform expressionData
 
-datExpr <- as.data.frame(t(wgcnaRawData));
+dataExpr <- as.data.frame(t(wgcnaRawData));
 
 
 
+# data cleaning
+
+# adopted from docs
+gsg = goodSamplesGenes(dataExpr, verbose = 3);
+
+
+
+if (!gsg$allOK)
+{
+# Optionally, print the gene and sample names that were removed:
+if (sum(!gsg$goodGenes)>0)
+printFlush(paste("Removing genes:", paste(names(datExpr0)[!gsg$goodGenes], collapse = ", ")));
+if (sum(!gsg$goodSamples)>0)
+printFlush(paste("Removing samples:", paste(rownames(datExpr0)[!gsg$goodSamples], collapse = ", ")));
+# Remove the offending genes and samples from the data:
+dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
+}
+
 
 
 
-- 
cgit v1.2.3


From 42c120dff2b3cac8a6b6546ebab9daf021aac11a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 22:42:43 +0300
Subject: compute the softthreshhold

---
 scripts/wgcna_analysis.R | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 8e90d7d..cb93492 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -5,15 +5,12 @@ stringsAsFactors = FALSE
 
 # load expression data **assumes csv format row(traits)(columns info+samples)
 
-
 wgcnaRawData <- read.csv(file = "wgcna_data.csv")
 
 # transform expressionData
 
 dataExpr <- as.data.frame(t(wgcnaRawData));
 
-
-
 # data cleaning
 
 # adopted from docs
@@ -32,6 +29,17 @@ printFlush(paste("Removing samples:", paste(rownames(datExpr0)[!gsg$goodSamples]
 dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
 }
 
+# network constructions and modules
+
+# choose softthreshhold (Calculate soft threshold if the user specified the)
+
+powers = c(c(1:10), seq(from = 12, to=20, by=2)) 
+sft = pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
+
+
+
+
+
 
 
 
-- 
cgit v1.2.3


From 1c98a10bf5015a85b856f9e937417d51ec05d781 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 22:49:43 +0300
Subject: construct  gene co-expression  network & module detection

---
 scripts/wgcna_analysis.R | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index cb93492..29f0259 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -33,9 +33,26 @@ dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
 
 # choose softthreshhold (Calculate soft threshold if the user specified the)
 
-powers = c(c(1:10), seq(from = 12, to=20, by=2)) 
-sft = pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
-
+powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
+sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
+
+# pass user options
+network <- blockwiseModules(dataExpr,
+                  #similarity  matrix options
+                  corType = "pearson",
+                  #adjacency  matrix options
+
+                  power = sft$powerEstimate,
+                  networkType = "unsigned",
+                  #TOM options
+                  TOMtype =  "unsigned",
+
+                  #module indentification
+
+                  minmodulesSize = 30,
+                  deepSplit = 5,
+                  PamRespectsDendro = FALSE
+                )
 
 
 
-- 
cgit v1.2.3


From b32f4ee074d55d8ab78863d4c5acc652ec9cd839 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 23:18:18 +0300
Subject: plot plotDendroAndColors and generate png

---
 scripts/wgcna_analysis.R | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 29f0259..65ff36e 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -54,6 +54,24 @@ network <- blockwiseModules(dataExpr,
                   PamRespectsDendro = FALSE
                 )
 
+# plot dendro add color
+
+# Convert labels to colors for plotting
+mergedColors = labels2colors(net$colors)
+# Plot the dendrogram and the module colors underneath 
+
+
+# generate random name for png && save the image location
+
+
+
+png("WGCNAoutput.png",width=1000,height=600,type='cairo-png')
+
+plotDendroAndColors(network$dendrograms[[1]],mergedColors[net$blockGenes[[1]]],
+"Module colors",
+dendroLabels = FALSE, hang = 0.03,
+addGuide = TRUE, guideHang = 0.05)
+
 
 
 
-- 
cgit v1.2.3


From 49b852baa46c0f06caa2f0621b18d521cf334483 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 23:40:17 +0300
Subject: function to generate rand str for image

---
 scripts/wgcna_analysis.R | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 65ff36e..efe0336 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -1,7 +1,9 @@
 # initial workspace setup
 
 library(WGCNA);
-stringsAsFactors = FALSE
+library(stringi);
+
+options(stringsAsFactors = FALSE);
 
 # load expression data **assumes csv format row(traits)(columns info+samples)
 
@@ -64,8 +66,18 @@ mergedColors = labels2colors(net$colors)
 # generate random name for png && save the image location
 
 
+genImageRandStr <- function(prefix){
+
+	randStr <- paste(prefix,stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_")
+
+	return(paste(randStr,".png",sep=""))
+}
+
+
+
+png(genImageRandStr,width=1000,height=600,type='cairo-png')
+
 
-png("WGCNAoutput.png",width=1000,height=600,type='cairo-png')
 
 plotDendroAndColors(network$dendrograms[[1]],mergedColors[net$blockGenes[[1]]],
 "Module colors",
-- 
cgit v1.2.3


From 56092341abe9579b995ff6105722154183b31d22 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 14 Sep 2021 23:41:46 +0300
Subject: remove debug statements

---
 scripts/wgcna_analysis.R | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index efe0336..16a44fd 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -56,14 +56,6 @@ network <- blockwiseModules(dataExpr,
                   PamRespectsDendro = FALSE
                 )
 
-# plot dendro add color
-
-# Convert labels to colors for plotting
-mergedColors = labels2colors(net$colors)
-# Plot the dendrogram and the module colors underneath 
-
-
-# generate random name for png && save the image location
 
 
 genImageRandStr <- function(prefix){
@@ -74,6 +66,7 @@ genImageRandStr <- function(prefix){
 }
 
 
+mergedColors = labels2colors(net$colors)
 
 png(genImageRandStr,width=1000,height=600,type='cairo-png')
 
-- 
cgit v1.2.3


From e0f25dedea08842820424ced51af9af0c7eaab4b Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 15 Sep 2021 02:13:03 +0300
Subject: Fetch IMAGE_DIR env and add img location

---
 scripts/wgcna_analysis.R | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 16a44fd..54650df 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -1,10 +1,14 @@
 # initial workspace setup
 
+
+# todo pass required input data here
 library(WGCNA);
 library(stringi);
 
 options(stringsAsFactors = FALSE);
 
+imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
+
 # load expression data **assumes csv format row(traits)(columns info+samples)
 
 wgcnaRawData <- read.csv(file = "wgcna_data.csv")
@@ -33,7 +37,7 @@ dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
 
 # network constructions and modules
 
-# choose softthreshhold (Calculate soft threshold if the user specified the)
+# choose softthreshhold (Calculate soft threshold)
 
 powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
 sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
@@ -65,12 +69,12 @@ genImageRandStr <- function(prefix){
 	return(paste(randStr,".png",sep=""))
 }
 
+mergedColors <- labels2colors(net$colors)
 
-mergedColors = labels2colors(net$colors)
-
-png(genImageRandStr,width=1000,height=600,type='cairo-png')
+imageLoc <- file.path(imgDir,genImageRandStr("WGCNAoutput"))
 
 
+png(imageLoc,width=1000,height=600,type='cairo-png')
 
 plotDendroAndColors(network$dendrograms[[1]],mergedColors[net$blockGenes[[1]]],
 "Module colors",
@@ -79,9 +83,3 @@ addGuide = TRUE, guideHang = 0.05)
 
 
 
-
-
-
-
-
-
-- 
cgit v1.2.3


From 94e2e79141cbddb48456fb5707eb0e4e36e97d3b Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 15 Sep 2021 02:19:03 +0300
Subject: rename variables && delete debugs

---
 scripts/wgcna_analysis.R | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 54650df..390bee4 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -1,7 +1,3 @@
-# initial workspace setup
-
-
-# todo pass required input data here
 library(WGCNA);
 library(stringi);
 
@@ -11,15 +7,14 @@ imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
 
 # load expression data **assumes csv format row(traits)(columns info+samples)
 
-wgcnaRawData <- read.csv(file = "wgcna_data.csv")
+inputData <- read.csv(file = "wgcna_data.csv")
 
 # transform expressionData
 
-dataExpr <- as.data.frame(t(wgcnaRawData));
+dataExpr <- as.data.frame(t(inputData));
 
 # data cleaning
 
-# adopted from docs
 gsg = goodSamplesGenes(dataExpr, verbose = 3);
 
 
-- 
cgit v1.2.3


From cee10bacd4316eb807c36b8a11e84f9be5945f44 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 15 Sep 2021 04:34:26 +0300
Subject: minor fixes

---
 scripts/wgcna_analysis.R | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 390bee4..267cd86 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -1,3 +1,5 @@
+
+
 library(WGCNA);
 library(stringi);
 
@@ -6,6 +8,7 @@ options(stringsAsFactors = FALSE);
 imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
 
 # load expression data **assumes csv format row(traits)(columns info+samples)
+# pass the file_path as arg
 
 inputData <- read.csv(file = "wgcna_data.csv")
 
@@ -13,26 +16,29 @@ inputData <- read.csv(file = "wgcna_data.csv")
 
 dataExpr <- as.data.frame(t(inputData));
 
-# data cleaning
+## data cleaning
 
 gsg = goodSamplesGenes(dataExpr, verbose = 3);
 
-
+# https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/
 
 if (!gsg$allOK)
 {
-# Optionally, print the gene and sample names that were removed:
 if (sum(!gsg$goodGenes)>0)
-printFlush(paste("Removing genes:", paste(names(datExpr0)[!gsg$goodGenes], collapse = ", ")));
+printFlush(paste("Removing genes:", paste(names(dataExpr)[!gsg$goodGenes], collapse = ", ")));
 if (sum(!gsg$goodSamples)>0)
-printFlush(paste("Removing samples:", paste(rownames(datExpr0)[!gsg$goodSamples], collapse = ", ")));
+printFlush(paste("Removing samples:", paste(rownames(dataExpr)[!gsg$goodSamples], collapse = ", ")));
 # Remove the offending genes and samples from the data:
 dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
 }
 
-# network constructions and modules
+## network constructions and modules
+
+# Allow multi-threading within WGCNA
+enableWGCNAThreads()
 
 # choose softthreshhold (Calculate soft threshold)
+# xtodo allow users to pass args
 
 powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
 sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
-- 
cgit v1.2.3


From 3d36fe96c94cebb6e7ea93b735148b25c4b95f6d Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 12:22:10 +0300
Subject: load data  from json file and and convert to dt

---
 scripts/wgcna_analysis.R | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 267cd86..d0ba91a 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -2,26 +2,29 @@
 
 library(WGCNA);
 library(stringi);
+library(rjson)
 
 options(stringsAsFactors = FALSE);
 
 imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
 
-# load expression data **assumes csv format row(traits)(columns info+samples)
+# load expression data **assumes from json files row(traits)(columns info+samples)
 # pass the file_path as arg
 
-inputData <- read.csv(file = "wgcna_data.csv")
+results <- fromJSON(file = "file_path.json")
 
-# transform expressionData
+# trait_sample_data <- results$trait_sample_data
+trait_sample_data <- do.call(rbind, results$trait_sample_data)
 
-dataExpr <- as.data.frame(t(inputData));
 
-## data cleaning
+dataExpr <- data.frame(apply(trait_sample_data, 2, function(x) as.numeric(as.character(x))))
+# trait_sample_data <- as.data.frame(t(results$trait_sample_data))
+# transform expressionData
 
+dataExpr <- data.frame(t(dataExpr))
 gsg = goodSamplesGenes(dataExpr, verbose = 3);
 
 # https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/
-
 if (!gsg$allOK)
 {
 if (sum(!gsg$goodGenes)>0)
@@ -49,7 +52,7 @@ network <- blockwiseModules(dataExpr,
                   corType = "pearson",
                   #adjacency  matrix options
 
-                  power = sft$powerEstimate,
+                  power = 5,
                   networkType = "unsigned",
                   #TOM options
                   TOMtype =  "unsigned",
@@ -70,14 +73,13 @@ genImageRandStr <- function(prefix){
 	return(paste(randStr,".png",sep=""))
 }
 
-mergedColors <- labels2colors(net$colors)
+mergedColors <- labels2colors(network$colors)
 
 imageLoc <- file.path(imgDir,genImageRandStr("WGCNAoutput"))
 
-
 png(imageLoc,width=1000,height=600,type='cairo-png')
 
-plotDendroAndColors(network$dendrograms[[1]],mergedColors[net$blockGenes[[1]]],
+plotDendroAndColors(network$dendrograms[[1]],mergedColors[network$blockGenes[[1]]],
 "Module colors",
 dendroLabels = FALSE, hang = 0.03,
 addGuide = TRUE, guideHang = 0.05)
-- 
cgit v1.2.3


From 95620e1aef5a9c56875845769d58d2aab20dacca Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 12:37:51 +0300
Subject: pass other variables from user input for network constr

---
 scripts/wgcna_analysis.R | 23 +++++++++++++++--------
 1 file changed, 15 insertions(+), 8 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index d0ba91a..73d0e3f 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -13,12 +13,19 @@ imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
 
 results <- fromJSON(file = "file_path.json")
 
-# trait_sample_data <- results$trait_sample_data
-trait_sample_data <- do.call(rbind, results$trait_sample_data)
 
+# parse the json data input
+
+minModuleSize <-results$minModuleSize
+
+TOMtype <-results$TOMtype
+
+corType <-results$corType
+# 
+
+trait_sample_data <- do.call(rbind, results$trait_sample_data)
 
 dataExpr <- data.frame(apply(trait_sample_data, 2, function(x) as.numeric(as.character(x))))
-# trait_sample_data <- as.data.frame(t(results$trait_sample_data))
 # transform expressionData
 
 dataExpr <- data.frame(t(dataExpr))
@@ -49,18 +56,18 @@ sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
 # pass user options
 network <- blockwiseModules(dataExpr,
                   #similarity  matrix options
-                  corType = "pearson",
+                  corType = corType,
                   #adjacency  matrix options
 
                   power = 5,
                   networkType = "unsigned",
                   #TOM options
-                  TOMtype =  "unsigned",
+                  TOMtype =  TOMtype,
 
                   #module indentification
 
-                  minmodulesSize = 30,
-                  deepSplit = 5,
+                  minmodulesSize = minModuleSize,
+                  deepSplit = 3,
                   PamRespectsDendro = FALSE
                 )
 
@@ -76,7 +83,7 @@ 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]]],
-- 
cgit v1.2.3


From 4a8e40f7331f61ba8b7038e8ad48f86018ac7dc6 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 12:47:27 +0300
Subject: pass json file path as an arg

---
 scripts/wgcna_analysis.R | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 73d0e3f..53b59d5 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -7,11 +7,20 @@ library(rjson)
 options(stringsAsFactors = FALSE);
 
 imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
-
 # 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) {
+  stop("Argument for the file location is requires", call.=FALSE)
+} else {
+  # default output file
+  json_file_path  = args[1]
+}
 
-results <- fromJSON(file = "file_path.json")
+results <- fromJSON(file = json_file_path)
 
 
 # parse the json data input
-- 
cgit v1.2.3


From 655343aded3ece533f267bd9fd16aadf0cefff02 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 12:49:40 +0300
Subject: add mock test data for script

---
 scripts/wgcna_test_data.csv  |  9 +++++++
 scripts/wgcna_test_data.json | 64 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 73 insertions(+)
 create mode 100644 scripts/wgcna_test_data.csv
 create mode 100644 scripts/wgcna_test_data.json

(limited to 'scripts')

diff --git a/scripts/wgcna_test_data.csv b/scripts/wgcna_test_data.csv
new file mode 100644
index 0000000..8db9598
--- /dev/null
+++ b/scripts/wgcna_test_data.csv
@@ -0,0 +1,9 @@
+129S1/SvImJ,A/J,AKR/J,B6D2F1,BALB/cByJ,BALB/cJ
+7.142,7.31,7.49,6.899,7.172,7.396
+7.071,7.05,7.313,6.999,7.293,7.117
+7.221,7.246,7.754,6.866,6.752,7.269
+9.221,9.246,9.954,6.866,6.952,9.269
+7.221,7.246,7.754,6.866,6.752,7.269
+7.221,7.246,7.754,6.866,6.752,7.269
+11.221,11.246,11.1154,6.866,6.1152,11.269
+
diff --git a/scripts/wgcna_test_data.json b/scripts/wgcna_test_data.json
new file mode 100644
index 0000000..7348b4e
--- /dev/null
+++ b/scripts/wgcna_test_data.json
@@ -0,0 +1,64 @@
+{
+   "trait_sample_data":[
+  {
+    "129S1/SvImJ": 7.142,
+    "A/J": 7.31,
+    "AKR/J": 7.49,
+    "B6D2F1": 6.899,
+    "BALB/cByJ": 7.172,
+    "BALB/cJ": 7.396
+  },
+  {
+    "129S1/SvImJ": 7.071,
+    "A/J": 7.05,
+    "AKR/J": 7.313,
+    "B6D2F1": 6.999,
+    "BALB/cByJ": 7.293,
+    "BALB/cJ": 7.117
+  },
+  {
+    "129S1/SvImJ": 7.221,
+    "A/J": 7.246,
+    "AKR/J": 7.754,
+    "B6D2F1": 6.866,
+    "BALB/cByJ": 6.752,
+    "BALB/cJ": 7.269
+  },
+  {
+    "129S1/SvImJ": 9.221,
+    "A/J": 9.246,
+    "AKR/J": 9.954,
+    "B6D2F1": 6.866,
+    "BALB/cByJ": 6.952,
+    "BALB/cJ": 9.269
+  },
+  {
+    "129S1/SvImJ": 7.221,
+    "A/J": 7.246,
+    "AKR/J": 7.754,
+    "B6D2F1": 6.866,
+    "BALB/cByJ": 6.752,
+    "BALB/cJ": 7.269
+  },
+  {
+    "129S1/SvImJ": 7.221,
+    "A/J": 7.246,
+    "AKR/J": 7.754,
+    "B6D2F1": 6.866,
+    "BALB/cByJ": 6.752,
+    "BALB/cJ": 7.269
+  },
+  {
+    "129S1/SvImJ": 11.221,
+    "A/J": 11.246,
+    "AKR/J": 11.1154,
+    "B6D2F1": 6.866,
+    "BALB/cByJ": 6.1152,
+    "BALB/cJ": 11.269
+  }
+   ],
+   "TOMtype": "unsigned",
+   "minModuleSize": 30,
+   "corType": "pearson"
+
+}
\ No newline at end of file
-- 
cgit v1.2.3


From 9216b6ae956b5c78a9b6d21dbd40b6df1e111264 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 14:22:14 +0300
Subject: validate required output

---
 scripts/wgcna_analysis.R | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

(limited to 'scripts')

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")
\ No newline at end of file
-- 
cgit v1.2.3


From eb2277a5fc96795bf6432e392e62601a3cf94058 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 14:22:31 +0300
Subject: sample output data

---
 scripts/output.json | 161 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 161 insertions(+)
 create mode 100644 scripts/output.json

(limited to 'scripts')

diff --git a/scripts/output.json b/scripts/output.json
new file mode 100644
index 0000000..9caf837
--- /dev/null
+++ b/scripts/output.json
@@ -0,0 +1,161 @@
+{
+   "ModEigens":{
+      "MEturquoise":[
+         0.0646677768085351,
+         0.137200224277058,
+         0.63451113720732,
+         -0.544002665501479,
+         -0.489487590361863,
+         0.197111117570427
+      ]
+   },
+   "soft_threshold":{
+      "Power":[
+         1,
+         2,
+         3,
+         4,
+         5,
+         6,
+         7,
+         8,
+         9,
+         10,
+         12,
+         14,
+         16,
+         18,
+         20
+      ],
+      "SFT.R.sq":[
+         0.0181093215847335,
+         0.00011984142485113,
+         0.000171967046945159,
+         0.0105462010616537,
+         0.0341444584348834,
+         0.0687163726151286,
+         0.0306423506274298,
+         0.0492567394226327,
+         0.0789539269997996,
+         0.0944880158122527,
+         0.122195040270446,
+         0.0340768567186139,
+         0.0625860126119281,
+         0.100082257137014,
+         0.128277841930818
+      ],
+      "slope":[
+         3.81011386139005,
+         -0.170826531149538,
+         0.159161787390082,
+         -1.01047981107833,
+         -1.55943531024794,
+         -1.93420125756514,
+         -1.16799247295814,
+         -1.33414063070555,
+         -1.54984944650438,
+         -1.54715757057087,
+         -1.49931213589121,
+         -1.80460140377151,
+         -2.19055343583319,
+         -2.52135805259606,
+         -2.58599487577447
+      ],
+      "truncated.R.sq":[
+         0.768989700952805,
+         0.522025793450566,
+         0.329341226670409,
+         0.110265719555879,
+         0.0195649645183151,
+         -0.0503253079741786,
+         0.0507498358330625,
+         -0.0129255450167765,
+         -0.035717519210676,
+         -0.0807094793662766,
+         -0.0967803564932559,
+         0.00172686282662393,
+         -0.0340811003657508,
+         -0.0390284600100592,
+         -0.0489269837827069
+      ],
+      "mean.k.":[
+         4.20178789454309,
+         3.44556816856968,
+         2.98532344074325,
+         2.65297323828966,
+         2.39517682414009,
+         2.18846935370095,
+         2.01963258852289,
+         1.87999059876872,
+         1.76335304166057,
+         1.66510080962817,
+         1.51038968360321,
+         1.39583176924843,
+         1.30882729664563,
+         1.24120316437299,
+         1.18753154238216
+      ],
+      "median.k.":[
+         4.65733789933094,
+         4.13585224131512,
+         3.75980713552836,
+         3.43775457512904,
+         3.15305040369031,
+         2.89933881967523,
+         2.67225531456956,
+         2.46825611568646,
+         2.28437024155601,
+         2.118086531192,
+         1.83011067501282,
+         1.59073325345641,
+         1.38991168639473,
+         1.2201000051609,
+         1.07553194658444
+      ],
+      "max.k.":[
+         4.81522245318686,
+         4.21987143583501,
+         3.83876962723542,
+         3.55526976885104,
+         3.32904938849614,
+         3.14312441404036,
+         2.98828051379132,
+         2.85837136671219,
+         2.74879840851137,
+         2.65594228759455,
+         2.50929962297015,
+         2.40113981571731,
+         2.31993775805391,
+         2.25792900175825,
+         2.2098218130451
+      ]
+   },
+   "blockGenes":[
+      1,
+      2,
+      3,
+      4,
+      5,
+      6,
+      7
+   ],
+   "net_colors":{
+      "X1":"turquoise",
+      "X2":"turquoise",
+      "X3":"turquoise",
+      "X4":"turquoise",
+      "X5":"turquoise",
+      "X6":"turquoise",
+      "X7":"turquoise"
+   },
+   "net_unmerged":{
+      "X1":"turquoise",
+      "X2":"turquoise",
+      "X3":"turquoise",
+      "X4":"turquoise",
+      "X5":"turquoise",
+      "X6":"turquoise",
+      "X7":"turquoise"
+   },
+   "imageLoc":"/WGCNAoutput_1uujpTIpC.png"
+}
\ No newline at end of file
-- 
cgit v1.2.3


From fc335fa1394a39d1f9f397cb69c755040ecfc5e1 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 14:37:48 +0300
Subject: append input to output

---
 scripts/wgcna_analysis.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

(limited to 'scripts')

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
-- 
cgit v1.2.3


From 9c221e0d89603acd5412be95650a469824e2ab99 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 15:10:16 +0300
Subject: check for na powerEst and use a default value

---
 scripts/wgcna_analysis.R | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index ee749e9..c3b1ac8 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -62,13 +62,21 @@ enableWGCNAThreads()
 powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
 sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
 
+# check the power estimate
+
+if (is.na(sft$powerEstimate)){
+  powerEst = 1
+}else{
+  powerEst = sft$powerEstimate
+}
+
 # pass user options
 network <- blockwiseModules(dataExpr,
                   #similarity  matrix options
                   corType = corType,
                   #adjacency  matrix options
 
-                  power = 5,
+                  power = powerEst,
                   networkType = "unsigned",
                   #TOM options
                   TOMtype =  TOMtype,
-- 
cgit v1.2.3


From 3062aee581560ae1928d8e6077366fc072646677 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 21:27:42 +0300
Subject: add traits as columns names and pass as json input

---
 scripts/wgcna_analysis.R     | 18 +++++++++++-------
 scripts/wgcna_test_data.json |  3 ++-
 2 files changed, 13 insertions(+), 8 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index c3b1ac8..e641652 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -53,6 +53,8 @@ dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
 
 ## network constructions and modules
 
+names(dataExpr) = inputData$trait_names
+
 # Allow multi-threading within WGCNA
 enableWGCNAThreads()
 
@@ -82,6 +84,7 @@ network <- blockwiseModules(dataExpr,
                   TOMtype =  TOMtype,
 
                   #module indentification
+                  verbose = 3,
 
                   minmodulesSize = minModuleSize,
                   deepSplit = 3,
@@ -108,13 +111,14 @@ dendroLabels = FALSE, hang = 0.03,
 addGuide = TRUE, guideHang = 0.05)
 
 
-
-
-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$unmergedColors,
-  imageLoc=imageLoc))
+json_data <- list(input = inputData,
+  output = list(ModEigens=network$MEs,
+   soft_threshold=sft$fitIndices,
+   blockGenes =network$blockGenes[[1]],
+   net_colors =network$colors,
+   power_used_for_analy=powerEst,
+   net_unmerged=network$unmergedColors,
+   imageLoc=imageLoc))
 
 json_data <- toJSON(json_data)
 
diff --git a/scripts/wgcna_test_data.json b/scripts/wgcna_test_data.json
index 7348b4e..1d469f4 100644
--- a/scripts/wgcna_test_data.json
+++ b/scripts/wgcna_test_data.json
@@ -1,4 +1,5 @@
 {
+  "trait_names":["1455537_at","1425637_at","1449593_at","1421945_a_at","1450423_s_at","1423841_at","1451144_at"],
    "trait_sample_data":[
   {
     "129S1/SvImJ": 7.142,
@@ -61,4 +62,4 @@
    "minModuleSize": 30,
    "corType": "pearson"
 
-}
\ No newline at end of file
+}
-- 
cgit v1.2.3


From 6f25b8e2b1d1a34c054d325b1c37b303529b8827 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 27 Sep 2021 15:15:28 +0300
Subject: remove unnecessary comments and variables

---
 scripts/wgcna_analysis.R | 18 ++++--------------
 1 file changed, 4 insertions(+), 14 deletions(-)

(limited to 'scripts')

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index e641652..17b3537 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -23,24 +23,14 @@ if (length(args)==0) {
 inputData <- fromJSON(file = json_file_path)
 
 
-# parse the json data input
-
-minModuleSize <-inputData$minModuleSize
-
-TOMtype <-inputData$TOMtype
-
-corType <-inputData$corType
-# 
-
 trait_sample_data <- do.call(rbind, inputData$trait_sample_data)
 
 dataExpr <- data.frame(apply(trait_sample_data, 2, function(x) as.numeric(as.character(x))))
 # transform expressionData
 
 dataExpr <- data.frame(t(dataExpr))
-gsg = goodSamplesGenes(dataExpr, verbose = 3);
+gsg = goodSamplesGenes(dataExpr, verbose = 3)
 
-# https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/
 if (!gsg$allOK)
 {
 if (sum(!gsg$goodGenes)>0)
@@ -75,18 +65,18 @@ if (is.na(sft$powerEstimate)){
 # pass user options
 network <- blockwiseModules(dataExpr,
                   #similarity  matrix options
-                  corType = corType,
+                  corType = inputData$corType,
                   #adjacency  matrix options
 
                   power = powerEst,
                   networkType = "unsigned",
                   #TOM options
-                  TOMtype =  TOMtype,
+                  TOMtype =  inputData$TOMtype,
 
                   #module indentification
                   verbose = 3,
 
-                  minmodulesSize = minModuleSize,
+                  minmodulesSize = inputData$minModuleSize,
                   deepSplit = 3,
                   PamRespectsDendro = FALSE
                 )
-- 
cgit v1.2.3