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tests: fix unit test
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@jorainer
jorainer committed Nov 14, 2024
1 parent 7bd035d commit 6d5b344
Showing 1 changed file with 27 additions and 22 deletions.
49 changes: 27 additions & 22 deletions tests/testthat/test_XcmsExperimentHdf5.R
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Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,7 @@ test_that("findChromPeaks,XcmsExperimentHdf5 works", {
a <- as(xmse_h5, "MsExperiment")
a <- as(a, "XcmsExperimentHdf5")
h5_file <- tempfile()
.h5_initialize_file(h5_file)
xcms:::.h5_initialize_file(h5_file)
a@hdf5_file <- h5_file
a@sample_id <- c("S1", "S2", "S3")
p <- xmse_h5@processHistory[[1L]]@param
Expand Down Expand Up @@ -150,14 +150,14 @@ test_that("refineChromPeaks,XcmsExperimentHdf5,MergeNeighboringPeaksParam", {

af <- tempfile()
ref <- loadXcmsData("faahko_sub2")
a <- .xcms_experiment_to_hdf5(ref, af)
a <- xcms:::.xcms_experiment_to_hdf5(ref, af)
res <- refineChromPeaks(a, MergeNeighboringPeaksParam())
expect_error(validObject(a))
expect_true(validObject(res))
## Compare results from both. Need chromPeaks() function first.
ref <- refineChromPeaks(ref, MergeNeighboringPeaksParam())
ref_pks <- chromPeaks(ref)
res_pks <- .h5_read_data(res@hdf5_file, id = res@sample_id,
res_pks <- xcms:::.h5_read_data(res@hdf5_file, id = res@sample_id,
ms_level = rep(1L, length(res)),
read_colnames = TRUE, read_rownames = TRUE)
res_pks <- do.call(
Expand Down Expand Up @@ -186,7 +186,7 @@ test_that("groupChromPeaks,featureDefinitions,XcmsExperimentHdf5 works", {
expect_true(hasFeatures(x, 1L))
expect_false(hasFeatures(x, 2L))
expect_false(hasFeatures(x, 1:2))
a <- .h5_read_data_frame("/features/ms_1/feature_definitions",
a <- xcms:::.h5_read_data_frame("/features/ms_1/feature_definitions",
x@hdf5_file, read_rownames = TRUE)
ref <- featureDefinitions(loadXcmsData("xmse"))
ref$peakidx <- NULL
Expand All @@ -195,7 +195,7 @@ test_that("groupChromPeaks,featureDefinitions,XcmsExperimentHdf5 works", {
rownames(ref) <- NULL
expect_true(all(colnames(ref) %in% colnames(a)))
expect_equal(ref, a[, colnames(ref)])
pks <- .h5_chrom_peaks(x, msLevel = 1L)
pks <- xcms:::.h5_chrom_peaks(x, msLevel = 1L)
for (i in seq_along(pks)) {
b <- .h5_read_matrix(paste0("/S", i, "/ms_1/feature_to_chrom_peaks"),
x@hdf5_file)
Expand Down Expand Up @@ -239,19 +239,19 @@ test_that("featureValues,XcmsExperimentHdf5 etc works", {
nf <- nrow(b)
rtmed <- b$rtmed
## .h5_feature_values_sample
a <- .h5_feature_values_sample(
a <- xcms:::.h5_feature_values_sample(
xmseg_full_h5@hdf5_file, sample_id = "S1", ms_level = 1L,
n_features = nf, method = "sum", filled = FALSE, col_idx = 9L)
b <- unname(featureValues(ref, method = "sum", value = "maxo",
filled = FALSE)[, 1L])
expect_equal(a, b)
a <- .h5_feature_values_sample(
a <- xcms:::.h5_feature_values_sample(
xmseg_full_h5@hdf5_file, sample_id = "S4", ms_level = 1L,
n_features = nf, filled = FALSE, method = "maxint", col_idx = c(7L, 9L))
b <- unname(featureValues(ref, method = "maxint", value = "into",
filled = FALSE, intensity = "maxo")[, 4L])
expect_equal(a, b)
a <- .h5_feature_values_sample(
a <- xcms:::.h5_feature_values_sample(
xmseg_full_h5@hdf5_file, sample_id = "S4", ms_level = 1L,
n_features = nf, filled = FALSE, method = "medret", col_idx = c(8L, 4L),
rtmed = rtmed)
Expand All @@ -260,15 +260,15 @@ test_that("featureValues,XcmsExperimentHdf5 etc works", {
expect_equal(a, b)

## .h5_feature_values_ms_level
a <- .h5_feature_values_ms_level(1L, xmseg_full_h5, method = "medret",
a <- xcms:::.h5_feature_values_ms_level(1L, xmseg_full_h5, method = "medret",
value = "into", filled = FALSE)
b <- featureValues(ref, method = "medret", value = "into", filled = FALSE)
expect_equal(unname(a), unname(b))
a <- .h5_feature_values_ms_level(1L, xmseg_full_h5, method = "sum",
a <- xcms:::.h5_feature_values_ms_level(1L, xmseg_full_h5, method = "sum",
value = "maxo", filled = FALSE)
b <- featureValues(ref, method = "sum", value = "maxo", filled = FALSE)
expect_equal(unname(a), unname(b))
a <- .h5_feature_values_ms_level(1L, xmseg_full_h5, method = "maxint",
a <- xcms:::.h5_feature_values_ms_level(1L, xmseg_full_h5, method = "maxint",
value = "sn", intensity = "into",
filled = FALSE)
b <- featureValues(ref, method = "maxint", value = "sn", intensity = "into",
Expand Down Expand Up @@ -345,11 +345,11 @@ test_that("adjustRtime,XcmsExperimentHdf5 and related function work", {
dropFeatureDefinitions() |>
applyAdjustedRtime()
res_h5 <- tempfile()
res <- .xcms_experiment_to_hdf5(ref, res_h5)
res <- xcms:::.xcms_experiment_to_hdf5(ref, res_h5)
## Create a single sample XcmsExperimentHdf5
a <- ref[3L]
a_h5 <- tempfile()
a <- .xcms_experiment_to_hdf5(a, a_h5)
a <- xcms:::.xcms_experiment_to_hdf5(a, a_h5)
## Perform retention time alignment on reference data
ref <- ref |>
groupChromPeaks(pdp, msLevel = 1L) |>
Expand All @@ -362,7 +362,7 @@ test_that("adjustRtime,XcmsExperimentHdf5 and related function work", {

############################################################################
## .h5_update_rt_chrom_peaks_sample: adjust rt of chrom peaks:
cnt <- .h5_update_rt_chrom_peaks_sample(
cnt <- xcms:::.h5_update_rt_chrom_peaks_sample(
a@sample_id[1L], rt_raw, rt_adj, 1L, a@hdf5_file)
expect_equal(cnt, a@hdf5_mod_count + 1L)
a@hdf5_mod_count <- cnt
Expand Down Expand Up @@ -448,18 +448,23 @@ test_that("chromatogram,XcmsExperimentHdf5 works", {
expect_true(all(unlist(featureDefinitions(res)$peakidx) %in%
seq_len(nrow(chromPeaks(res)))))
ref <- chromatogram(
xmseg_full_ref,
mz = chromPeaks(xmseg_full_h5)[1:5, c("mzmin", "mzmax")],
rt = chromPeaks(xmse_full_h5)[1:5, c("rtmin", "rtmax")])
xmseg_full_ref,mz = chromPeaks(xmseg_full_h5)[1:5, c("mzmin", "mzmax")],
rt = chromPeaks(xmseg_full_h5)[1:5, c("rtmin", "rtmax")],
chunkSize = 2L, BPPARAM = bpparam(), msLevel = 1L,
aggregationFun = "sum", isolationWindow = NULL,
chromPeaks = "apex_within", return.type = "XChromatograms")
a <- featureDefinitions(res)
b <- featureDefinitions(res)
b <- featureDefinitions(ref)
rownames(a) <- NULL
rownames(b) <- NULL
expect_true(all(colnames(a) %in% colnames(b)))
expect_equal(unname(a[, colnames(b)]), unname(b[, colnames(b)]))
expect_equal(a[, colnames(b)], b[, colnames(b)])

## MS2 data.
res <- chromatogram(xmseg_full_h5, msLevel = 2L,
mz = chromPeaks(xmse_full_h5)[1:5, c("mzmin", "mzmax")],
rt = chromPeaks(xmse_full_h5)[1:5, c("rtmin", "rtmax")])
res <- chromatogram(
xmseg_full_h5, msLevel = 2L,
mz = chromPeaks(xmseg_full_h5)[1:5, c("mzmin", "mzmax")],
rt = chromPeaks(xmseg_full_h5)[1:5, c("rtmin", "rtmax")])
expect_true(validObject(res))
expect_true(length(intensity(res[[1L]])) == 0)
expect_true(length(intensity(res[[2L]])) == 0)
Expand Down

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