comparison tests/univariate_tests.R @ 0:ef64d3752050 draft

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

0:ef64d3752050

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")