Skip to content

Commit

Permalink
create test for filterEmptySpectra
Browse files Browse the repository at this point in the history
  • Loading branch information
@tnaake
tnaake committed Aug 11, 2023
1 parent 8bbad8b commit f17bf10
Showing 1 changed file with 99 additions and 1 deletion.
100 changes: 99 additions & 1 deletion tests/testthat/test_function_calculateMetrics_from_Spectra.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,44 @@ metrics_spectra_2_vals <- c(2.594770e+02, 0, 2.505386e-01,
4.999981e-01, 7.505367e-01, 1.000000e+00, 5.052683e-02, -5.673914e-01,
-4.700149e-01, 9.310000e02, 6.229579e+08, 0)

## create small test spectra to test filterEmptySpectra
spd <- DataFrame(
msLevel = c(2L, 2L, 2L),
polarity = c(1L, 1L, 1L),
name = c("comp_1", "comp_2", "comp_3"))
## Assign m/z and intensity values
spd$mz <- list(
c(109.2),
c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16),
c())
spd$intensity <- list(
c(0),
c(6.685, 4.381, 3.022, 16.708, 100.0, 4.565, 40.643),
c())
spd$rtime <- c(9.44, 9.44, 15.84)
sps_empty <- Spectra(spd)
spd$mz <- list(
c(109.2, 124.2, 124.5, 170.16, 170.52),
c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16),
c())
spd$intensity <- list(
c(0, 0, 0, 0, 0),
c(6.685, 4.381, 3.022, 16.708, 100.0, 4.565, 40.643),
c())
spd$rtime <- c(9.44, 9.44, 15.84)
sps_multiple_empty <- Spectra(spd)
spd$mz <- list(
c(109.2, 124.2, 124.5, 170.16, 170.52),
c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16),
c(56.0494, 69.0447, 83.0603, 109.0395, 110.0712,
111.0551, 123.0429, 138.0662, 195.0876))
spd$intensity <- list(
c(3.407, 47.494, 3.094, 100.0, 13.240),
c(6.685, 4.381, 3.022, 16.708, 100.0, 4.565, 40.643),
c(0.459, 2.585, 2.446, 0.508, 8.968, 0.524, 0.974, 100.0, 40.994))
spd$rtime <- c(9.44, 9.44, 15.84)
sps_not_empty <- Spectra(spd)

test_that("calculateMetricsFromOneSampleSpectra", {
## spectra
expect_error(
Expand Down Expand Up @@ -108,6 +146,26 @@ test_that("calculateMetricsFromOneSampleSpectra", {
metrics = "msSignal10xChange", change = c("jump", "fall")),
"'change' has to be of length 1")

## test filterEmptySpectra
expect_equal(as.numeric(calculateMetricsFromOneSampleSpectra(
spectra = sps_empty, metrics = "numberSpectra",
filterEmptySpectra = FALSE, msLevel = 2L)), 3)
expect_equal(as.numeric(calculateMetricsFromOneSampleSpectra(
spectra = sps_empty, metrics = "numberSpectra",
filterEmptySpectra = TRUE, msLevel = 2L)), 1)
expect_equal(as.numeric(calculateMetricsFromOneSampleSpectra(
spectra = sps_multiple_empty, metrics = "numberSpectra",
filterEmptySpectra = FALSE, msLevel = 2L)), 3)
expect_equal(as.numeric(calculateMetricsFromOneSampleSpectra(
spectra = sps_multiple_empty, metrics = "numberSpectra",
filterEmptySpectra = TRUE, msLevel = 2L)), 1)
expect_equal(as.numeric(calculateMetricsFromOneSampleSpectra(
spectra = sps_not_empty, metrics = "numberSpectra",
filterEmptySpectra = FALSE, msLevel = 2L)), 3)
expect_equal(as.numeric(calculateMetricsFromOneSampleSpectra(
spectra = sps_not_empty, metrics = "numberSpectra",
filterEmptySpectra = TRUE, msLevel = 2L)), 3)

## test attributes
expect_equal(attr(metrics_spectra_1, "names"), colnames_metrics)
expect_equal(attr(metrics_spectra_1_filtered, "names"), colnames_metrics)
Expand Down Expand Up @@ -205,6 +263,26 @@ test_that("calculateMetricsFromSpectra", {
metrics = "msSignal10xChange", change = c("jump", "fall")),
"'change' has to be of length 1")

## test filterEmptySpectra
expect_equal(as.numeric(calculateMetricsFromSpectra(
spectra = sps_empty, metrics = "numberSpectra",
filterEmptySpectra = FALSE, msLevel = 2L)), 3)
expect_equal(as.numeric(calculateMetricsFromSpectra(
spectra = sps_empty, metrics = "numberSpectra",
filterEmptySpectra = TRUE, msLevel = 2L)), 1)
expect_equal(as.numeric(calculateMetricsFromSpectra(
spectra = sps_multiple_empty, metrics = "numberSpectra",
filterEmptySpectra = FALSE, msLevel = 2L)), 3)
expect_equal(as.numeric(calculateMetricsFromSpectra(
spectra = sps_multiple_empty, metrics = "numberSpectra",
filterEmptySpectra = TRUE, msLevel = 2L)), 1)
expect_equal(as.numeric(calculateMetricsFromSpectra(
spectra = sps_not_empty, metrics = "numberSpectra",
filterEmptySpectra = FALSE, msLevel = 2L)), 3)
expect_equal(as.numeric(calculateMetricsFromSpectra(
spectra = sps_not_empty, metrics = "numberSpectra",
filterEmptySpectra = TRUE, msLevel = 2L)), 3)

## test attributes
expect_equal(attr(metrics_spectra, "names"), NULL)
expect_equal(attr(metrics_spectra_filtered, "names"), NULL)
Expand Down Expand Up @@ -265,7 +343,7 @@ metrics_msexp_filtered <- calculateMetricsFromMsExperiment(msexp = msexp,
metrics = metrics, filterEmptySpectra = FALSE, msLevel = 1,
relativeTo = "Q1", mode = "TIC", change = "jump")

test_that("calculateMetricsFrom<sExperiment", {
test_that("calculateMetricsFromMsExperiment", {
expect_equal(dim(metrics_msexp), c(2, 12))
expect_equal(dim(metrics_msexp_filtered), c(2, 12))
dirs <- unlist(lapply(
Expand Down Expand Up @@ -421,6 +499,26 @@ test_that("calculateMetrics", {
expect_error(calculateMetrics(msexp, metrics = "foo"),
"should be one of ")

## test filterEmptySpectra
expect_equal(as.numeric(calculateMetrics(object = sps_empty,
metrics = "numberSpectra", filterEmptySpectra = FALSE,
msLevel = 2L)), 3)
expect_equal(as.numeric(calculateMetrics(object = sps_empty,
metrics = "numberSpectra", filterEmptySpectra = TRUE,
msLevel = 2L)), 1)
expect_equal(as.numeric(calculateMetrics(object = sps_multiple_empty,
metrics = "numberSpectra", filterEmptySpectra = FALSE,
msLevel = 2L)), 3)
expect_equal(as.numeric(calculateMetrics(object = sps_multiple_empty,
metrics = "numberSpectra", filterEmptySpectra = TRUE,
msLevel = 2L)), 1)
expect_equal(as.numeric(calculateMetrics(object = sps_not_empty,
metrics = "numberSpectra", filterEmptySpectra = FALSE,
msLevel = 2L)), 3)
expect_equal(as.numeric(calculateMetrics(object = sps_not_empty,
metrics = "numberSpectra", filterEmptySpectra = TRUE,
msLevel = 2L)), 3)

## test attributes
expect_equal(attributes(metrics_spectra_wrapper)$dimnames[[2]],
colnames_metrics)
Expand Down

0 comments on commit f17bf10

Please sign in to comment.