data("GlobalPatterns", package = "phyloseq")
GA <- subset_taxa(GlobalPatterns, Phylum == "Acidobacteria")
krona_error_or_not <- try(system("ktImportText 2>&1", intern = TRUE))
if (class(krona_error_or_not) == "try-error") {
skip_on_cran()
skip_on_os("windows")
test_that("krona send an error when krona is not installed", {
expect_warning(krona(GA, "Number.of.sequences.html"))
expect_warning(krona(GA, "Number.of.ASVs.html", nb_seq = FALSE))
expect_warning(merge_krona(c("Number.of.sequences.html", "Number.of.ASVs.html")))
})
} else {
test_that("krona function works fine with GlobalPatterns dataset", {
skip_on_cran()
skip_on_os("windows")
testFolder <- tempdir()
suppressWarnings(unlink(list.files(testFolder, full.names = TRUE), recursive = TRUE))
expect_silent(krona(GA, file = paste0(testFolder, "/Number.of.sequences.html")))
expect_silent(krona(GA, file = paste0(testFolder, "/Number.of.ASVs.html"), nb_seq = FALSE))
expect_silent(merge_krona(
c(
paste0(testFolder, "/Number.of.sequences.html"),
paste0(testFolder, "/Number.of.ASVs.html")
),
output = paste0(testFolder, "/mergeKrona.html")
))
unlink(list.files(testFolder, full.names = TRUE), recursive = TRUE)
})
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.