diff tests/univariate_tests.R @ 0:ef64d3752050 draft

planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/univariate_tests.R	Wed Jul 27 11:44:34 2016 -0400
@@ -0,0 +1,194 @@
+library(RUnit)
+
+wrapperF <- function(argVc) {
+
+
+    source("../univariate_script.R")
+
+
+#### Start_of_testing_code <- function() {}
+
+
+    ##------------------------------
+    ## Initializing
+    ##------------------------------
+
+    ## options
+    ##--------
+
+    strAsFacL <- options()$stringsAsFactors
+    options(stringsAsFactors = FALSE)
+
+    ## packages
+    ##---------
+
+    library(PMCMR)
+
+    ## constants
+    ##----------
+
+    modNamC <- "Univariate" ## module name
+
+    topEnvC <- environment()
+    flagC <- "\n"
+
+    ## functions
+    ##----------
+
+    flgF <- function(tesC,
+                     envC = topEnvC,
+                     txtC = NA) { ## management of warning and error messages
+
+        tesL <- eval(parse(text = tesC), envir = envC)
+
+        if(!tesL) {
+
+            sink(NULL)
+            stpTxtC <- ifelse(is.na(txtC),
+                              paste0(tesC, " is FALSE"),
+                              txtC)
+
+            stop(stpTxtC,
+                 call. = FALSE)
+
+        }
+
+    } ## flgF
+
+    ## log file
+    ##---------
+
+    sink(argVc["information"])
+
+    cat("\nStart of the '", modNamC, "' Galaxy module call: ",
+        format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
+
+    ## loading
+    ##--------
+
+    datMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
+                                    check.names = FALSE,
+                                    header = TRUE,
+                                    row.names = 1,
+                                    sep = "\t")))
+
+    samDF <- read.table(argVc["sampleMetadata_in"],
+                        check.names = FALSE,
+                        header = TRUE,
+                        row.names = 1,
+                        sep = "\t")
+
+    varDF <- read.table(argVc["variableMetadata_in"],
+                        check.names = FALSE,
+                        header = TRUE,
+                        row.names = 1,
+                        sep = "\t")
+
+    tesC <- argVc["tesC"]
+
+    ## checking
+    ##---------
+
+    flgF("identical(rownames(datMN), rownames(samDF))", txtC = "Column names of the dataMatrix are not identical to the row names of the sampleMetadata; check your data with the 'Check Format' module in the 'Quality Control' section")
+    flgF("identical(colnames(datMN), rownames(varDF))", txtC = "Row names of the dataMatrix are not identical to the row names of the variableMetadata; check your data with the 'Check Format' module in the 'Quality Control' section")
+
+    flgF("argVc['facC'] %in% colnames(samDF)", txtC = paste0("Required factor of interest '", argVc['facC'], "' could not be found in the column names of the sampleMetadata"))
+    flgF("mode(samDF[, argVc['facC']]) %in% c('character', 'numeric')", txtC = paste0("The '", argVc['facC'], "' column of the sampleMetadata should contain either number only, or character only"))
+
+    flgF("!(tesC %in% c('ttest', 'wilcoxon')) || (mode(samDF[, argVc['facC']]) == 'character' && length(unique(samDF[, argVc['facC']])) == 2)", txtC = paste0("For 'ttest' and 'wilcoxon', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain characters with only two different classes"))
+    flgF("!(tesC %in% c('anova', 'kruskal')) || (mode(samDF[, argVc['facC']]) == 'character' && length(unique(samDF[, argVc['facC']])) > 2)", txtC = paste0("For 'anova' and 'kruskal', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain characters with at least three different classes"))
+    flgF("!(tesC %in% c('pearson', 'spearman')) || mode(samDF[, argVc['facC']]) == 'numeric'", txtC = paste0("For 'pearson' and 'spearman', the chosen factor column ('", argVc['facC'], "') of the sampleMetadata should contain numbers only"))
+
+    flgF("argVc['adjC'] %in% c('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none')")
+
+    flgF("0 <= as.numeric(argVc['thrN']) && as.numeric(argVc['thrN']) <= 1",
+         txtC = "(corrected) p-value threshold must be between 0 and 1")
+
+
+    ##------------------------------
+    ## Computation
+    ##------------------------------
+
+
+    varDF <- univariateF(datMN = datMN,
+                         samDF = samDF,
+                         varDF = varDF,
+                         facC = argVc["facC"],
+                         tesC = tesC,
+                         adjC = argVc["adjC"],
+                         thrN = as.numeric(argVc["thrN"]))
+
+
+    ##------------------------------
+    ## Ending
+    ##------------------------------
+
+
+    ## saving
+    ##--------
+
+    varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
+                              varDF)
+    write.table(varDF,
+                file = argVc["variableMetadata_out"],
+                quote = FALSE,
+                row.names = FALSE,
+                sep = "\t")
+
+    ## closing
+    ##--------
+
+    cat("\nEnd of '", modNamC, "' Galaxy module call: ",
+        as.character(Sys.time()), "\n", sep = "")
+
+    sink()
+
+    options(stringsAsFactors = strAsFacL)
+
+
+
+#### End_of_testing_code <- function() {}
+
+
+    return(list(varDF = varDF))
+
+    rm(list = ls())
+
+}
+
+exaDirOutC <- "output"
+if(!file.exists(exaDirOutC))
+   stop("Please create an 'output' subfolder into the (current) 'tests' folder")
+
+tesArgLs <- list(input_kruskal = c(facC = "ageGroup",
+                     tesC = "kruskal",
+                     adjC = "fdr",
+                     thrN = "0.05",
+                     .chkC = "checkEqualsNumeric(outLs[['varDF']]['HMDB01032', 'ageGroup_kruskal_senior-experienced_pva'], 0.1231246, tolerance = 1e-6)"),
+                 example1_wilcoxDif = c(facC = "jour",
+                     tesC = "wilcoxon",
+                     adjC = "fdr",
+                     thrN = "0.05",
+                     .chkC = "checkEqualsNumeric(outLs[['varDF']]['MT3', 'jour_wilcoxon_J3-J10_dif'], 0.216480042, tolerance = 1e-8)"),
+                 example1_ttestFdr = c(facC = "jour",
+                     tesC = "ttest",
+                     adjC = "fdr",
+                     thrN = "0.05",
+                     .chkC = "checkEqualsNumeric(outLs[['varDF']]['MT3', 'jour_ttest_J3-J10_fdr'], 0.7605966, tolerance = 1e-6)"))
+
+for(tesC in names(tesArgLs))
+    tesArgLs[[tesC]] <- c(tesArgLs[[tesC]],
+                          dataMatrix_in = file.path(unlist(strsplit(tesC, "_"))[1], "dataMatrix.tsv"),
+                          sampleMetadata_in = file.path(unlist(strsplit(tesC, "_"))[1], "sampleMetadata.tsv"),
+                          variableMetadata_in = file.path(unlist(strsplit(tesC, "_"))[1], "variableMetadata.tsv"),
+                          variableMetadata_out = file.path(exaDirOutC, "variableMetadata.tsv"),
+                          information = file.path(exaDirOutC, "information.txt"))
+
+for(tesC in names(tesArgLs)) {
+    print(tesC)
+    outLs <- wrapperF(tesArgLs[[tesC]])
+    if(".chkC" %in% names(tesArgLs[[tesC]]))
+        stopifnot(eval(parse(text = tesArgLs[[tesC]][[".chkC"]])))
+}
+
+message("Checks successfully completed")