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.json | 64 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 scripts/wgcna_test_data.json

(limited to 'scripts/wgcna_test_data.json')

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 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/wgcna_test_data.json')

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