diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/calculate_biweight.R | 43 | ||||
| -rw-r--r-- | scripts/wgcna_analysis.R | 17 |
2 files changed, 15 insertions, 45 deletions
diff --git a/scripts/calculate_biweight.R b/scripts/calculate_biweight.R deleted file mode 100644 index 8d8366e..0000000 --- a/scripts/calculate_biweight.R +++ /dev/null @@ -1,43 +0,0 @@ - -library(testthat) -library(WGCNA) - -arg_values <- commandArgs(trailingOnly = TRUE) -ParseArgs <- function(args){ - - trait_vals <- as.numeric(unlist(strsplit(args[1], split=" "))) - target_vals <- as.numeric(unlist(strsplit(args[2], split=" "))) - - return(list(trait_vals= c(trait_vals),target_vals = c(target_vals))) - -} -BiweightMidCorrelation <- function(trait_val,target_val){ - - results <-bicorAndPvalue(as.numeric(unlist(trait_val)),as.numeric(unlist(target_val))) - return ((c(c(results$bicor)[1],c(results$p)[1]))) - -} - - - -test_that("biweight results"),{ - vec_1 <- c(1,2,3,4) - vec_2 <- c(1,2,3,4) - - results <- BiweightMidCorrelation(vec_1,vec_2) - expect_equal(c(1.0,0.0),results) -} - - -test_that("parsing args "),{ - my_args <- c("1 2 3 4","5 6 7 8") - results <- ParseArgs(my_args) - - expect_equal(results[1],c(1,2,3,4)) - expect_equal(results[2],c(5,6,7,8)) -} - -parsed_values <- ParseArgs(arg_values) - - -cat(BiweightMidCorrelation(parsed_values[1],parsed_values[2]))
\ No newline at end of file diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R index 17b3537..b0d25a9 100644 --- a/scripts/wgcna_analysis.R +++ b/scripts/wgcna_analysis.R @@ -6,11 +6,13 @@ 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 +23,7 @@ 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 +86,11 @@ 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="_") @@ -90,14 +98,19 @@ genImageRandStr <- function(prefix){ return(paste(randStr,".png",sep="")) } + 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, +dendroLabels = NULL, hang = 0.03, addGuide = TRUE, guideHang = 0.05) |