Skip to content

Commit

Permalink
tests: rearrange tests
Browse files Browse the repository at this point in the history
  • Loading branch information
@ethanbass
ethanbass committed Dec 10, 2023
1 parent 46062b0 commit cf5732b
Show file tree
Hide file tree
Showing 3 changed files with 86 additions and 81 deletions.
4 changes: 2 additions & 2 deletions R/combine_peaks.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -93,9 +93,9 @@ merge_peaks <- function(peak_table, peaks, method = c("max", "sum")){
sel <- which.max(colMeans(peak_table$tab[, pks.idx], na.rm = TRUE))
sel.idx <- which(colnames(peak_table$tab) == peaks[sel])
if (method == "max"){
peak_table$tab[, sel.idx] <- do.call(pmax, peak_table$tab[, pks.idx])
peak_table$tab[[sel.idx]] <- do.call(pmax, peak_table$tab[, pks.idx])
} else if (method == "sum"){
peak_table$tab[, sel.idx] <- apply(pk_tab$tab[,c(pks.idx)],1,sum)
peak_table$tab[[sel.idx]] <- apply(pk_tab$tab[,pks.idx], 1, sum)
}
peak_table$tab <- peak_table$tab[, -pks.idx[-sel]]
peak_table$pk_meta <- peak_table$pk_meta[, -pks.idx[-sel]]
Expand Down
161 changes: 83 additions & 78 deletions tests/testthat/test-pipeline.R
View file
Original file line number Diff line number Diff line change
@@ -1,20 +1,5 @@
### test preprocess function ###
path <- "testdata/DAD1.CSV"
x <- read.csv(path, fileEncoding = "utf-16")
x1 <- suppressWarnings(load_chroms(path = path, format.in = "csv", find_files = FALSE))
folder <- "testdata"
x2 <- suppressWarnings(load_chroms(folder, format.in = "csv", find_files = TRUE))

test_that("load_chroms works", {
expect_equal(x[,2], x1[[1]][, "220.00000"], ignore_attr = TRUE)
expect_equal(x1, x2, ignore_attr = TRUE)
expect_equal(length(x1), length(path))
expect_error(suppressWarnings(load_chroms(path = "fake_path_that_doesn't_exist", format.in = "csv")))
expect_error(suppressWarnings(load_chroms(path = path, format.in = "invalid_format")))
})

data("Sa")
new.ts <- seq(10,18.66,by=.01) # choose time-points
new.ts <- seq(10, 18.66, by=.01) # choose time-points
new.lambdas <- seq(200, 318, by = 2) # choose wavelengths

out <- preprocess(X = Sa[[1]], dim1 = new.ts, dim2 = new.lambdas, show_progress = FALSE)
Expand Down Expand Up @@ -98,6 +83,7 @@ test_that("plot_chroms works to plot alignments", {
expect_error(plot_chroms(pktab))
})


test_that("plot_chroms works to plot alignments with ggplot", {
skip_on_cran()
skip_if_not_installed("vdiffr")
Expand Down Expand Up @@ -170,6 +156,7 @@ test_that("strip plot works", {

path <- system.file("extdata", "Sa_metadata.csv", package = "chromatographR")
meta <- read.csv(path)

pk_tab <- attach_metadata(pk_tab, metadata = meta, column = "vial")

test_that("attach_metadata works", {
Expand Down Expand Up @@ -215,14 +202,23 @@ test_that("combine_peaks works", {
expect_equal(rownames(pk_tab_c$tab), rownames(pk_tab$tab))
})

test_that("merge_peaks works", {
test_that("merge_peaks works with max method", {
pk_tab_m <- merge_peaks(pk_tab, peaks=c("V10","V11"))
expect_equal(pk_tab_m$tab$V11, pmax(pk_tab$tab$V10, pk_tab$tab$V11))
expect_equal(ncol(pk_tab_m), ncol(pk_tab)-1)
expect_equal(ncol(pk_tab_m$pk_meta), ncol(pk_tab$pk_meta)-1)
expect_equal(rownames(pk_tab_m$tab), rownames(pk_tab$tab))
})

# test_that("merge_peaks works with sum method", {
# data(pk_tab)
# pk_tab_m <- merge_peaks(pk_tab, peaks=c("V10","V11"), method = "sum")
# expect_equal(pk_tab_m$tab[["V11"]], (pk_tab$tab$V10 + pk_tab$tab$V11))
# expect_equal(ncol(pk_tab_m), ncol(pk_tab)-1)
# expect_equal(ncol(pk_tab_m$pk_meta), ncol(pk_tab$pk_meta)-1)
# expect_equal(rownames(pk_tab_m$tab), rownames(pk_tab$tab))
# })

test_that("normalize_data works", {
pk_tab_norm <- normalize_data(pk_tab, chrom_list = dat.pr, column = "mass")
expect_equal(rownames(pk_tab_norm$tab), rownames(pk_tab$tab))
Expand Down Expand Up @@ -252,7 +248,7 @@ test_that("plot.peak_list works", {
skip_if_not_installed("vdiffr")
plot_peaks <- function(){
plot(pks_egh, chrom_list = dat.pr, points = TRUE,
ticks = TRUE, lambda = 210)
ticks = TRUE, lambda = 210)
}
vdiffr::expect_doppelganger("plot.peak_list", plot_peaks)

Expand All @@ -269,6 +265,8 @@ test_that("plot.peak_list works", {
expect_error(plot(pks_egh, chrom_list = dat.pr, lambda=190))
})



test_that("plot.ptw_list works", {
skip_if_not_installed("vdiffr")
plot_ptw_list <- function(){
Expand Down Expand Up @@ -332,61 +330,6 @@ test_that("plot_spectrum works", {
expect_equal(ncol(x), 1)
})

test_that("plot_spectrum works with plotly engine", {
skip_on_cran()
skip_if_not_installed("vdiffr")
skip_if_not_installed("plotly")
skip_if_not_installed("reticulate")
skip_if_not_installed("rsvg")

p1 <- plot_spectrum("13.62", peak_table = pk_tab, chrom_list = dat.pr,
export_spectrum = FALSE, what = "rt", chr = 1,
verbose = FALSE, engine = "plotly")
expect_doppelganger_plotly("plot_both_plotly", p = p1)

p2 <- plot_spectrum("13.62", peak_table = pk_tab, chrom_list = dat.pr,
export_spectrum = FALSE, what="rt", chr=1,
verbose = FALSE, engine="plotly", plot_trace = FALSE)
expect_doppelganger_plotly("plot_trace_plotly", p = p2)

p3 <- plot_spectrum("13.62", peak_table = pk_tab, chrom_list = dat.pr,
export_spectrum = FALSE, what="rt", chr=1,
verbose = FALSE, engine="plotly", plot_spectrum = FALSE)
expect_doppelganger_plotly("plot_spectrum_plotly", p = p3)
})

test_that("plot_chroms works with plotly", {
skip_on_cran()
skip_if_not_installed("vdiffr")
skip_if_not_installed("plotly")
skip_if_not_installed("reticulate")
skip_if_not_installed("rsvg")
p <- plot_chroms(warp, lambdas="210", engine="plotly")
suppressWarnings(expect_doppelganger_plotly(name = "alignment_plotly", p = p))
})

test_that("plot_spectrum works with ggplot2", {
skip_on_cran()
skip_if_not_installed("vdiffr")
skip_if_not_installed("ggplot2")
skip_if_not_installed("cowplot")

p1 <- plot_spectrum("13.62", peak_table = pk_tab, chrom_list = dat.pr,
export_spectrum = FALSE, what="rt", chr=1,
verbose = FALSE, engine="ggplot")
vdiffr::expect_doppelganger(title = "plot_both_ggplot", fig = p1)

p2 <- plot_spectrum("13.62", peak_table = pk_tab, chrom_list = dat.pr,
export_spectrum = FALSE, what="rt", chr=1,
verbose = FALSE, engine="ggplot", plot_trace = FALSE)
vdiffr::expect_doppelganger(title = "plot_trace_ggplot", fig = p2)

p3 <- plot_spectrum("13.62", peak_table = pk_tab, chrom_list = dat.pr,
export_spectrum = FALSE, what="rt", chr=1,
verbose = FALSE, engine = "ggplot", plot_spectrum = FALSE)
vdiffr::expect_doppelganger(title = "plot_spectrum_ggplot", fig = p3)
})

test_that("plot_spectrum works", {
x <- plot_spectrum("V13", peak_table = pk_tab, chrom_list = dat.pr, export = TRUE,
what="peak", chr=1, verbose = FALSE)
Expand Down Expand Up @@ -416,6 +359,32 @@ test_that("plot_spectrum works", {
expect_error(plot_spectrum(loc=12, peak_table = pk_tab, chrom_list = dat.pr, what="rt", engine="plotly"))
})


test_that("plot_spectrum works with ggplot2", {
skip_on_cran()
skip_if_not_installed("vdiffr")
skip_if_not_installed("ggplot2")
skip_if_not_installed("cowplot")

# generates empty pdf
# p1 <- plot_spectrum("13.62", peak_table = pk_tab, chrom_list = dat.pr,
# export_spectrum = FALSE, what="rt", chr=1,
# verbose = FALSE, engine="ggplot")
# vdiffr::expect_doppelganger(title = "plot_both_ggplot", fig = p1)

p2 <- plot_spectrum("13.62", peak_table = pk_tab, chrom_list = dat.pr,
export_spectrum = FALSE, what="rt", chr=1,
verbose = FALSE, engine="ggplot", plot_trace = FALSE)
vdiffr::expect_doppelganger(title = "plot_trace_ggplot", fig = p2)

p3 <- plot_spectrum("13.62", peak_table = pk_tab, chrom_list = dat.pr,
export_spectrum = FALSE, what="rt", chr=1,
verbose = FALSE, engine = "ggplot", plot_spectrum = FALSE)
vdiffr::expect_doppelganger(title = "plot_spectrum_ggplot", fig = p3)
})



test_that("mirror_plot works", {
skip_if_not_installed("vdiffr")
mirror1 <- function(){
Expand Down Expand Up @@ -458,8 +427,8 @@ test_that("plot_peak.list works", {
test_that("cluster_spectra works", {
skip_on_cran()
cl <- cluster_spectra(pk_tab, chrom_list = dat.pr, nboot = 10,
parallel = FALSE, verbose = FALSE, save = FALSE,
output = "both", plot_dend = FALSE, plot_spectra = FALSE)
parallel = FALSE, verbose = FALSE, save = FALSE,
output = "both", plot_dend = FALSE, plot_spectra = FALSE)
expect_equal(class(cl[[1]]), "pvclust")
expect_equal(class(cl[[2]]), "list")
})
Expand All @@ -474,10 +443,10 @@ test_that("write_peaktable writes csvs correctly", {
write_peaktable(peak_table = pk_tab, path = path, format = "csv", what=c("tab", "pk_meta"))
path_table <- paste0(file.path(path,"peak_table-tab"), ext =".csv")
path_meta <- paste0(file.path(path,"peak_table-pk_meta"), ext =".csv")

expect_true(file.exists(path_table))
expect_true(file.exists(path_meta))

expect_equal(pk_tab$tab, read.csv(file = path_table, row.names = 1), ignore_attr=TRUE)
expect_equal(pk_tab$pk_meta, read.csv(file = path_meta, row.names = 1), ignore_attr=TRUE)
expect_error(write_peaktable(pk_tab, path="fake_path"))
Expand All @@ -489,10 +458,46 @@ test_that("write_peaktable writes xlsx correctly", {
data(pk_tab)
path <- tempdir()
on.exit(unlink(c(fs::path(path, "peak_table", ext="xlsx"), path)))

write_peaktable(pk_tab, path = path, format = "xlsx")
file <- fs::path(path, "peak_table", ext = "xlsx")
xx <- openxlsx::read.xlsx(file, sheet = 1, rowNames = TRUE)
expect_equal(pk_tab$tab, xx, ignore_attr=TRUE)
expect_equal(pk_tab$pk_meta, openxlsx::read.xlsx(file, sheet = 2, rowNames = TRUE), ignore_attr=TRUE)
})

# Sys.setenv("VISUAL_TESTS" = "true")

test_that("plot_spectrum works with plotly engine", {
skip_on_cran()
skip_if_not_installed("vdiffr")
skip_if_not_installed("plotly")
skip_if_not_installed("reticulate")
skip_if_not_installed("rsvg")

p1 <- plot_spectrum("13.62", peak_table = pk_tab, chrom_list = dat.pr,
export_spectrum = FALSE, what = "rt", chr = 1,
verbose = FALSE, engine = "plotly")
expect_doppelganger_plotly("plot_both_plotly", p = p1)

p2 <- plot_spectrum("13.62", peak_table = pk_tab, chrom_list = dat.pr,
export_spectrum = FALSE, what="rt", chr=1,
verbose = FALSE, engine="plotly", plot_trace = FALSE)
expect_doppelganger_plotly("plot_trace_plotly", p = p2)

p3 <- plot_spectrum("13.62", peak_table = pk_tab, chrom_list = dat.pr,
export_spectrum = FALSE, what="rt", chr=1,
verbose = FALSE, engine="plotly", plot_spectrum = FALSE)
expect_doppelganger_plotly("plot_spectrum_plotly", p = p3)
})

test_that("plot_chroms works with plotly", {
skip_on_cran()
skip_if_not_installed("vdiffr")
skip_if_not_installed("plotly")
skip_if_not_installed("reticulate")
skip_if_not_installed("rsvg")

p <- plot_chroms(warp, lambdas="210", engine="plotly")
suppressWarnings(expect_doppelganger_plotly(name = "alignment_plotly", p = p))
})
2 changes: 1 addition & 1 deletion tests/testthat/test-utility-functions.R
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#### test utilities
#### test utilities ####
data(Sa_pr)

test_that("get_times works as expected", {
Expand Down

0 comments on commit cf5732b

Please sign in to comment.