tests/testthat/test_reading-writing.R

In SciDoPhenIA/phenomis: Analysis of single and multiple phenomic data sets

testthat::context("Testing 'read-write'")

testthat::test_that(".reading", {
  
  sacdir.c <- system.file("extdata/W4M00001_Sacurine-statistics", package = "phenomis")
  
  sacurine.se1 <- phenomis:::.reading(sacdir.c)
  
  testthat::expect_true(class(sacurine.se1) == "SummarizedExperiment")
  
  testthat::expect_equal(assay(sacurine.se1)[1, 1],
                         477491,
                         tolerance = 1e-3)
  # alternatively
  sacurine.se2 <- phenomis:::.reading(NA,
                                      file.path(sacdir.c, "Galaxy1_dataMatrix.tabular"),
                                      file.path(sacdir.c, "Galaxy2_sampleMetadata.tabular"),
                                      file.path(sacdir.c, "Galaxy3_variableMetadata.tabular"))
  
  testthat::expect_true(class(sacurine.se2) == "SummarizedExperiment")
  
  testthat::expect_equal(assay(sacurine.se2)[1, 1],
                         477491,
                         tolerance = 1e-3)
  
  
  testthat::expect_error(phenomis:::.reading(NA,
                                             file.path(sacdir.c, "Galaxy1_dataMatrix.tsv"),
                                             file.path(sacdir.c, "Galaxy2_sampleMetadata.tabular"),
                                             file.path(sacdir.c, "Galaxy3_variableMetadata.tabular")))
  
})

testthat::test_that("reading_SummarizedExperiment", {
  
  sacdir.c <- system.file("extdata/W4M00001_Sacurine-statistics", package = "phenomis")
  
  sacurine.se2 <- reading(sacdir.c)
  
  testthat::expect_true(class(sacurine.se2) == "SummarizedExperiment")
  
  testthat::expect_equal(assay(sacurine.se2)[1, 1],
                         477491,
                         tolerance = 1e-3)
  # alternatively
  sacurine.se3 <- reading(NA,
                          files.ls = list(dataMatrix = file.path(sacdir.c, "Galaxy1_dataMatrix.tabular"),
                                          sampleMetadata = file.path(sacdir.c, "Galaxy2_sampleMetadata.tabular"),
                                          variableMetadata = file.path(sacdir.c, "Galaxy3_variableMetadata.tabular")))
  
  testthat::expect_true(class(sacurine.se3) == "SummarizedExperiment")
  
  testthat::expect_equal(assay(sacurine.se3)[1, 1],
                         477491,
                         tolerance = 1e-3)
  
  
  testthat::expect_error(reading(NA,
                                 files.ls = list(dataMatrix = file.path(sacdir.c, "Galaxy1_dataMatrix.tsv"),
                                                 sampleMetadata = file.path(sacdir.c, "Galaxy2_sampleMetadata.tabular"),
                                                 variableMetadata = file.path(sacdir.c, "Galaxy3_variableMetadata.tabular"))))
  
})

testthat::test_that("reading_MultiAssayExperiment", {
  
  prometis_dir.c <- system.file("extdata/prometis", package = "phenomis")
  
  prometis.mae <- reading(prometis_dir.c)
  
  testthat::expect_true(class(prometis.mae) == "MultiAssayExperiment")
  
  testthat::expect_identical(names(prometis.mae), c("metabolomics", "proteomics"))
  
  testthat::expect_equal(MultiAssayExperiment::assays(prometis.mae)[["metabolomics"]][1, 1],
                         5.576,
                         tolerance = 1e-3)
  
  
  met.mae <- reading(prometis_dir.c, subsets.vc = "metabolomics")
  
  testthat::expect_true(class(met.mae) == "MultiAssayExperiment")
  
  testthat::expect_identical(names(met.mae), "metabolomics")
  
  testthat::expect_equal(MultiAssayExperiment::assays(met.mae)[["metabolomics"]][1, 1],
                         5.576,
                         tolerance = 1e-3)

})


testthat::test_that("reading_MultiDataSet", {
  
  prometis_dir.c <- system.file("extdata/prometis", package = "phenomis")
  
  prometis.mset1 <- reading(prometis_dir.c, output.c = "set")
  
  testthat::expect_true(class(prometis.mset1) == "MultiDataSet")
  
  testthat::expect_identical(names(prometis.mset1), c("metabolomics", "proteomics"))
  
  testthat::expect_equal(Biobase::exprs(prometis.mset1[["metabolomics"]])[1, 1],
                         5.576,
                         tolerance = 1e-3)
  
  
  prometis.mset2 <- reading(NA,
                            files.ls = list(metabolomics = list(dataMatrix = file.path(prometis_dir.c, "metabolomics", "dataMatrix.tsv"),
                                                                sampleMetadata = file.path(prometis_dir.c, "metabolomics", "sampleMetadata.tsv"),
                                                                variableMetadata = file.path(prometis_dir.c, "metabolomics", "variableMetadata.tsv")),
                                            proteomics = list(dataMatrix = file.path(prometis_dir.c, "proteomics", "dataMatrix.tsv"),
                                                              sampleMetadata = file.path(prometis_dir.c, "proteomics", "sampleMetadata.tsv"),
                                                              variableMetadata = file.path(prometis_dir.c, "proteomics", "variableMetadata.tsv"))),
                            output.c = "set")
  
  testthat::expect_true(class(prometis.mset2) == "MultiDataSet")
  
  testthat::expect_identical(names(prometis.mset2), c("metabolomics", "proteomics"))
  
  testthat::expect_equal(Biobase::exprs(prometis.mset2[["metabolomics"]])[1, 1],
                         5.576,
                         tolerance = 1e-3)
  
  # testthat::expect_identical(colnames(Biobase::pData(prometis.mset2[["metabolomics"]])), c("gene", "id"))
  
  
  
  metMset1 <- reading(prometis_dir.c, subsets.vc = "metabolomics", output.c = "set")
  
  testthat::expect_true(class(metMset1) == "MultiDataSet")
  
  testthat::expect_identical(names(metMset1), "metabolomics")
  
  testthat::expect_equal(Biobase::exprs(metMset1[["metabolomics"]])[1, 1],
                         5.576,
                         tolerance = 1e-3)
  
  
  metMset2 <- reading(NA,
                      files.ls = list(metabolomics = list(dataMatrix = file.path(prometis_dir.c, "metabolomics", "dataMatrix.tsv"),
                                                          sampleMetadata = file.path(prometis_dir.c, "metabolomics", "sampleMetadata.tsv"),
                                                          variableMetadata = file.path(prometis_dir.c, "metabolomics", "variableMetadata.tsv")),
                                      proteomics = list(dataMatrix = file.path(prometis_dir.c, "proteomics", "dataMatrix.tsv"),
                                                        sampleMetadata = file.path(prometis_dir.c, "proteomics", "sampleMetadata.tsv"),
                                                        variableMetadata = file.path(prometis_dir.c, "proteomics", "variableMetadata.tsv"))),
                      subsets.vc = "metabolomics", output.c = "set")
  
  testthat::expect_true(class(metMset2) == "MultiDataSet")
  
  testthat::expect_identical(names(metMset2), "metabolomics")
  
  testthat::expect_equal(Biobase::exprs(metMset2[["metabolomics"]])[1, 1],
                         5.576,
                         tolerance = 1e-3)
  
  
  testthat::expect_error(reading(NA,
                                 list(metabolomics = list(dataMatrix = file.path(prometis_dir.c, "metabolomics", "dataMatrix.tsv_XXX"),
                                                          sampleMetadata = file.path(prometis_dir.c, "metabolomics", "sampleMetadata.tsv"),
                                                          variableMetadata = file.path(prometis_dir.c, "metabolomics", "variableMetadata.tsv")),
                                      proteomics = list(dataMatrix = file.path(prometis_dir.c, "proteomics", "dataMatrix.tsv_XXX"),
                                                        sampleMetadata = file.path(prometis_dir.c, "proteomics", "sampleMetadata.tsv"),
                                                        variableMetadata = file.path(prometis_dir.c, "proteomics", "variableMetadata.tsv"))),
                                 output.c = "set"))
  
  testthat::expect_warning(reading(NA,
                                   list(metabolomics = list(dataMatrix = file.path(prometis_dir.c, "metabolomics", "dataMatrix.tsv"),
                                                            sampleMetadata = file.path(prometis_dir.c, "metabolomics", "sampleMetadata.tsv_XXX"),
                                                            variableMetadata = file.path(prometis_dir.c, "metabolomics", "variableMetadata.tsv")),
                                        proteomics = list(dataMatrix = file.path(prometis_dir.c, "proteomics", "dataMatrix.tsv"),
                                                          sampleMetadata = file.path(prometis_dir.c, "proteomics", "sampleMetadata.tsv"),
                                                          variableMetadata = file.path(prometis_dir.c, "proteomics", "variableMetadata.tsv"))),
                                   output.c = "set"))
  
  # testthat::expect_true(colnames(Biobase::pData(prometis.mset3[["metabolomics"]])) == "id")
  
  
})

testthat::test_that("writing_MultiDataSet", {
  
  prometis_dir.c <- system.file("extdata/prometis", package = "phenomis")
  
  prometis.mset4 <- reading(prometis_dir.c, output.c = "set")
  
  testthat::expect_error(writing(prometis.mset4,
                                 dir.c = NA,
                                 files.ls = list(metabolomics = list(dataMatrix = NA,
                                                                     sampleMetadata = file.path(getwd(), "metabolomics_sampleMetadata.tsv"),
                                                                     variableMetadata = file.path(getwd(), "metabolomics_variableMetadata.tsv")),
                                                 proteomics = list(dataMatrix = file.path(getwd(), "proteomics_dataMatrix.tsv"),
                                                                   sampleMetadata = file.path(getwd(), "proteomics_sampleMetadata.tsv"),
                                                                   variableMetadata = file.path(getwd(), "proteomics_variableMetadata.tsv")))))
  
})