tests/testRPPASet.R

In SuperCurve: RPPA Analysis Package

###
### $Id: testRPPASet.R 945 2015-01-21 00:06:51Z proebuck $
###


options(warn=1)
library(SuperCurve)
library(robustbase)
library(boot)
source("checkFuncs")


## Attempt to make comparisons easier
sys_tempdir <- file.path("", "tmp")
if (file.exists(sys_tempdir) &&
    file.info(sys_tempdir)$isdir &&
    file.access(sys_tempdir, 2) == 0) {
    Sys.setenv(TMPDIR=sys_tempdir)
}

## create project directory in per-session temporary directory
## Cannot successfully test without this...
persessionprojdir <- file.path(tempdir(), "supercurve")
if (!dir.create(persessionprojdir)) {
    stop("cannot create per-session project directory")
}

extdata.dir <- system.file("extdata", package="SuperCurveSampleData")
path <- file.path(extdata.dir, "rppaTumorData")
designfile <- file.path(path, "slidedesign.tsv")
designparams <- RPPADesignParams(grouping="blockSample",
                                 center=TRUE,
                                 designfile=designfile)
fitparams <- RPPAFitParams(measure="Mean.Net",
                           model="logistic",
                           method="nlrob",
                           ignoreNegative=FALSE,
                           warnLevel=-1)
normparams <- RPPANormalizationParams(method="vs")

rppaset <- RPPASet(path,
                   designparams,
                   fitparams,
                   normparams=normparams,
                   antibodyfile="proteinAssay.tsv")

###########################
## tests of path

checkException(RPPASet(path=5),
               msg="invalid value should fail")

checkException(RPPASet(path=c("results1", "results2")),
               msg="character vector should fail")

nosuchdir <- file.path(persessionprojdir, "nosuch")
checkException(RPPASet(path=nosuchdir),
               msg="nonexistent directory should fail")

filenotdir <- file.path(persessionprojdir, "somefile")
file.create(filenotdir)
checkException(RPPASet(path=filenotdir),
               msg="not a directory should fail")

emptydir <- file.path(persessionprojdir, "emptydir")
dir.create(emptydir)
checkException(RPPASet(path=emptydir,
                       designparams,
                       fitparams,
                       normparams=normparams),
               msg="directory without quantification files should fail")

###########################
## tests of designparams, fitparams, and normparams

checkException(RPPASet(path,
                       designparams=fitparams),
               msg="invalid object should fail")
checkException(RPPASet(path,
                       designparams,
                       fitparams=RPPAFitParams(measure="bogus"),
                       normparams=normparams),
               msg="fitparams with invalid measure should fail")
checkException(RPPASet(path,
                       designparams,
                       fitparams,
                       normparams=RPPANormalizationParams(method="bogus")),
               msg="normparams with unregistered method should fail")


###########################
## tests of antibodyfile

checkException(RPPASet(path=path,
                       designparams,
                       fitparams,
                       normparams=normparams,
                       antibodyfile=5),
               msg="invalid value should fail")

checkException(RPPASet(path=path,
                       designparams,
                       fitparams,
                       normparams=normparams,
                       antibodyfile=c("results1", "results2")),
               msg="character vector should fail")

checkException(RPPASet(path=path,
                       designparams,
                       fitparams,
                       normparams=normparams,
                       antibodyfile=""),
               msg="empty string should fail")

nosuchfile <- "nosuch.tsv"
checkException(RPPASet(path=path,
                       designparams,
                       fitparams,
                       normparams=normparams,
                       antibodyfile=nosuchfile),
               msg="nonexistent file should fail")

checkException(RPPASet(path=path,
                       designparams,
                       fitparams,
                       normparams=normparams,
                       antibodyfile=path),
               msg="directory instead of file should fail")

local({
    emptyfile <- file.path(persessionprojdir, "emptyfile.tsv")
    close(fconn <- file(emptyfile, "w"))

    checkException(RPPASet(path=path,
                           designparams,
                           fitparams,
                           normparams=normparams,
                           antibodyfile=emptyfile),
                   msg="empty file should fail")
})

local({
    singlecolfile <- file.path(persessionprojdir, "singlecolfile.tsv")
    fconn <- file(singlecolfile, "w")
    cat("Filename", file=fconn, sep="\n")
    for (filename in list.files(path)) {
        cat(filename, file=fconn, sep="\n")
    }
    close(fconn)

    checkException(RPPASet(path=path,
                           designparams,
                           fitparams,
                           normparams=normparams,
                           antibodyfile=singlecolfile),
                   msg="file with single column should fail")
})

local({
    missingreqdcolsfile <- file.path(persessionprojdir, "missingreqdcols.tsv")
    fconn <- file(missingreqdcolsfile, "w")
    cat(paste("Filename", "Size", sep="\t"), file=fconn, sep="\n")
    for (filename in list.files(path)) {
        filesize <- file.info(file.path(path, filename))$size
        cat(paste(filename, filesize, sep="\t"),
            file=fconn, sep="\n")
    }
    close(fconn)

    checkException(RPPASet(path=path,
                           designparams,
                           fitparams,
                           normparams=normparams,
                           antibodyfile=missingreqdcolsfile),
                   msg="file without required columns should fail")
})


###########################
## tests of summary rppaset

outdir <- file.path(persessionprojdir, "results")
dir.create(outdir)
checkException(write.summary(designparams,
                             path=outdir),
               msg="invalid object should fail")

###########################
## tests of summary path

checkException(write.summary(rppaset,
                             path=nosuchdir),
               msg="nonexistent output directory should fail")

switch(.Platform$OS.type,
       unix={
           readonlydir <- file.path(persessionprojdir, "readonly")
           dir.create(readonlydir, mode="0555")
           checkException(write.summary(rppaset,
                                        path=readonlydir),
                          msg="readonly output directory should fail")
       },
       windows={
           cat("skipped readonly output directory test (not implemented)", "\n")
       })

###########################
## tests of summary prefix

checkException(write.summary(rppaset,
                             path=outdir,
                             prefix=5),
               msg="invalid value should fail")

checkException(write.summary(rppaset,
                             path=outdir,
                             prefix=c("a", "b")),
               msg="character vector should fail")

###########################
## tests of summary graphs

checkException(write.summary(rppaset,
                             path=outdir,
                             graphs="yellow"),
               msg="invalid value should fail")

checkException(write.summary(rppaset,
                             path=outdir,
                             graphs=c(FALSE, TRUE)),
               msg="logical vector should fail")


###########################
## tests of summary tiffdir

checkException(write.summary(rppaset,
                             path=outdir,
                             graphs=1,
                             tiffdir=pi),
               msg="invalid value should fail")

# :NOTE: numeric "graphs" value silently converted to logical
checkException(write.summary(rppaset,
                             path=outdir,
                             graphs=1,
                             tiffdir=c("results1", "results2")),
               msg="character vector should fail")

checkException(write.summary(rppaset,
                             path=outdir,
                             graphs=TRUE,
                             tiffdir=nosuchdir),
               msg="nonexistent directory should fail")

checkException(write.summary(rppaset,
                             path=outdir,
                             graphs=TRUE,
                             tiffdir=filenotdir),
               msg="not a directory should fail")

## :NOTE: If unspecified, "tiffdir" is assumed to be sibling of "path".
## As of version 1.3.4, the code substitutes the package's image directory
## if no sibling dir exists.

## :NOTE: If "tiffdir" contains no image files, error messages from the
## ImageMagick binary appear onscreen, but they are not considered errors
## as far as the R code goes - the return code isn't currently examined
## for external failures. As many TIFF images contain "unrecognized tags",
## this is handy for letting the code continue processing. When a file is
## missing, a "missing slide" image is automatically substituted.


###########################
## tests of summary (missing ImageMagick binary)

switch(.Platform$OS.type,
       unix={
           # Willing to try test if 'convert' executable is not in /usr/bin
           binary <- "convert"
           binarydir <- dirname(Sys.which(binary))
           usrbindir <- file.path("", "usr", "bin")
           if (!grepl(binarydir, sprintf("^%s", usrbindir), fixed=TRUE)) {

               ##--------------------------------------------------------------
               simulateMissingConvertBinary <- function() {
                   savePATH <- Sys.getenv("PATH")
                   on.exit(Sys.setenv("PATH"=savePATH))
                   Sys.setenv("PATH"=usrbindir)

                   tryCatch(write.summary(rppaset,
                                          path=outdir,
                                          graphs=TRUE,
                                          tiffdir=emptydir),
                            warning=function(w) {
                                errmsg <- paste("(converted from warning)",
                                                w$message)
                                signalCondition(simpleError(errmsg))
                            })
               }

               checkException(simulateMissingConvertBinary(),
                              msg="missing ImageMagick binary should fail")
           } else {
               cat("skipped ImageMagick test",
                   "-",
                   sQuote(binary),
                   "binary in",
                   dQuote(usrbindir),
                   "\n")
           }
       },
       windows={
           cat("skipped ImageMagick test (not implemented)", "\n")
       })


## test one that should work...
write.summary(rppaset,
              path=outdir,
              prefix="testing",
              graphs=FALSE)



## If you need to save the results for some reason...
if (FALSE) {
    savedir <- file.path(path.expand("~"), "supercurve", "results")
    if (!file.exists(savedir)) {
        if (!dir.create(savedir, recursive=TRUE)) {
            stop(sprintf("directory %s could not be created",
                         dQuote(savedir)))
        }
    }
    file.copy(list.files(path=outdir, full.names=TRUE),
              savedir,
              overwrite=TRUE)
}