diff heatmap_wrapper.R @ 0:ad06aeed02c9 draft

planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/heatmap_wrapper.R	Tue Aug 02 06:26:41 2016 -0400
@@ -0,0 +1,156 @@
+#!/usr/bin/env Rscript
+
+library(batch) ## parseCommandArgs
+
+source_local <- function(fname){
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep="/"))
+}
+
+source_local("heatmap_script.R")
+
+argVc <- unlist(parseCommandArgs(evaluate=FALSE))
+
+
+##------------------------------
+## Initializing
+##------------------------------
+
+## options
+##--------
+
+strAsFacL <- options()[["stringsAsFactors"]]
+options(stringsAsFactors=FALSE)
+
+## constants
+##----------
+
+modNamC <- "Heatmap" ## module name
+
+## log file
+##---------
+
+sink(argVc["information"])
+
+cat("\nStart of the '", modNamC, "' module: ",
+    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
+
+## loading
+##--------
+
+proMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
+                                check.names = FALSE,
+                                header = TRUE,
+                                row.names = 1,
+                                sep = "\t")))
+
+obsDF <- read.table(argVc["sampleMetadata_in"],
+                    check.names = FALSE,
+                    header = TRUE,
+                    row.names = 1,
+                    sep = "\t")
+
+feaDF <- read.table(argVc["variableMetadata_in"],
+                    check.names = FALSE,
+                    header = TRUE,
+                    row.names = 1,
+                    sep = "\t")
+
+## adding default parameter values
+##--------------------------------
+
+
+if(!("corMetC" %in% names(argVc)))
+    argVc["corMetC"] <- "pearson"
+if(!("aggMetC" %in% names(argVc)))
+    argVc["aggMetC"] <- "ward"
+if(!("colC" %in% names(argVc)))
+    argVc["colC"] <- "blueOrangeRed"
+if(!("scaL" %in% names(argVc)))
+    argVc["scaL"] <- "TRUE"
+if(!("cexN" %in% names(argVc)))
+    argVc["cexN"] <- "0.8"
+
+## checking
+##---------
+
+if(as.numeric(argVc["cutSamN"]) > nrow(proMN))
+    stop("Number of sample clusters must be inferior to the number of samples")
+if(as.numeric(argVc["cutVarN"]) > ncol(proMN))
+    stop("Number of variable clusters must be inferior to the number of variables")
+
+## printing arguments
+##-------------------
+
+cat("\nArguments used:\n\n")
+argMC <- as.matrix(argVc)
+colnames(argMC) <- "value"
+argDatVl <- grepl("\\.dat$", argVc) ## discarding dataset file names
+if(sum(argDatVl))
+    argMC <- argMC[!argDatVl, , drop = FALSE]
+print(argMC)
+
+
+##------------------------------
+## Computation
+##------------------------------
+
+
+heaLs <- heatmapF(proMN = proMN,
+                  obsDF = obsDF,
+                  feaDF = feaDF,
+                  disC = argVc["disC"],
+                  cutSamN = as.numeric(argVc["cutSamN"]),
+                  cutVarN = as.numeric(argVc["cutVarN"]),
+                  fig.pdfC = argVc["figure"],
+                  corMetC = argVc["corMetC"],
+                  aggMetC = argVc["aggMetC"],
+                  colC = argVc["colC"],
+                  scaL = as.logical(argVc["scaL"]),
+                  cexN = as.numeric(argVc["cexN"]))
+
+
+##------------------------------
+## Ending
+##------------------------------
+
+
+## saving
+##-------
+
+proDF <- cbind.data.frame(dataMatrix = colnames(heaLs[["proMN"]]),
+                          as.data.frame(t(heaLs[["proMN"]])))
+write.table(proDF,
+            file = argVc["dataMatrix_out"],
+            quote = FALSE,
+            row.names = FALSE,
+            sep = "\t")
+
+obsDF <- cbind.data.frame(sampleMetadata = rownames(heaLs[["obsDF"]]),
+                          heaLs[["obsDF"]])
+write.table(obsDF,
+            file = argVc["sampleMetadata_out"],
+            quote = FALSE,
+            row.names = FALSE,
+            sep = "\t")
+
+feaDF <- cbind.data.frame(variableMetadata = rownames(heaLs[["feaDF"]]),
+                          heaLs[["feaDF"]])
+write.table(feaDF,
+            file = argVc["variableMetadata_out"],
+            quote = FALSE,
+            row.names = FALSE,
+            sep = "\t")
+
+## Ending
+##-------
+
+cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
+    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep = "")
+
+sink()
+
+options(stringsAsFactors = strAsFacL)
+
+rm(list = ls())