Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/fix_rqtl_covariates

4 files changed, 350 insertions, 0 deletions

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
diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
new file mode 100644
index 0000000..17b3537
--- /dev/null
+++ b/scripts/wgcna_analysis.R
@@ -0,0 +1,115 @@
+
+
+library(WGCNA);
+library(stringi);
+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 required", call.=FALSE)
+} else {
+  # default output file
+  json_file_path  = args[1]
+}
+
+inputData <- fromJSON(file = json_file_path)
+
+
+trait_sample_data <- do.call(rbind, inputData$trait_sample_data)
+
+dataExpr <- data.frame(apply(trait_sample_data, 2, function(x) as.numeric(as.character(x))))
+# transform expressionData
+
+dataExpr <- data.frame(t(dataExpr))
+gsg = goodSamplesGenes(dataExpr, verbose = 3)
+
+if (!gsg$allOK)
+{
+if (sum(!gsg$goodGenes)>0)
+printFlush(paste("Removing genes:", paste(names(dataExpr)[!gsg$goodGenes], collapse = ", ")));
+if (sum(!gsg$goodSamples)>0)
+printFlush(paste("Removing samples:", paste(rownames(dataExpr)[!gsg$goodSamples], collapse = ", ")));
+# Remove the offending genes and samples from the data:
+dataExpr <- dataExpr[gsg$goodSamples, gsg$goodGenes]
+}
+
+## network constructions and modules
+
+names(dataExpr) = inputData$trait_names
+
+# Allow multi-threading within WGCNA
+enableWGCNAThreads()
+
+# choose softthreshhold (Calculate soft threshold)
+# xtodo allow users to pass args
+
+powers <- c(c(1:10), seq(from = 12, to=20, by=2)) 
+sft <- pickSoftThreshold(dataExpr, powerVector = powers, verbose = 5)
+
+# check the power estimate
+
+if (is.na(sft$powerEstimate)){
+  powerEst = 1
+}else{
+  powerEst = sft$powerEstimate
+}
+
+# pass user options
+network <- blockwiseModules(dataExpr,
+                  #similarity  matrix options
+                  corType = inputData$corType,
+                  #adjacency  matrix options
+
+                  power = powerEst,
+                  networkType = "unsigned",
+                  #TOM options
+                  TOMtype =  inputData$TOMtype,
+
+                  #module indentification
+                  verbose = 3,
+
+                  minmodulesSize = inputData$minModuleSize,
+                  deepSplit = 3,
+                  PamRespectsDendro = FALSE
+                )
+
+
+
+genImageRandStr <- function(prefix){
+
+	randStr <- paste(prefix,stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_")
+
+	return(paste(randStr,".png",sep=""))
+}
+
+mergedColors <- labels2colors(network$colors)
+
+imageLoc <- file.path(imgDir,genImageRandStr("WGCNAoutput"))
+png(imageLoc,width=1000,height=600,type='cairo-png')
+
+plotDendroAndColors(network$dendrograms[[1]],mergedColors[network$blockGenes[[1]]],
+"Module colors",
+dendroLabels = FALSE, hang = 0.03,
+addGuide = TRUE, guideHang = 0.05)
+
+
+json_data <- list(input = inputData,
+  output = list(ModEigens=network$MEs,
+   soft_threshold=sft$fitIndices,
+   blockGenes =network$blockGenes[[1]],
+   net_colors =network$colors,
+   power_used_for_analy=powerEst,
+   net_unmerged=network$unmergedColors,
+   imageLoc=imageLoc))
+
+json_data <- toJSON(json_data)
+
+write(json_data,file= json_file_path)
\ No newline at end of file
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..1d469f4
--- /dev/null
+++ b/scripts/wgcna_test_data.json
@@ -0,0 +1,65 @@
+{
+  "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,
+    "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"
+
+}