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cmirzayicmirzayi
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Merge pull request #32 from annemarie-sharp/update-tests
Initial commit with updated testthat files
2 parents 028352f + a533475 commit 28b0b19

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‎DESCRIPTION‎

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ggplot2,
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kableExtra
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Suggests:
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BiocStyle,
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BiocStyle,
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knitr,
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rmarkdown,
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broom,
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jtools
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jtools,
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testthat (>= 3.0.0)
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Remotes:
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waldronlab/BugSigDBStats,
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waldronlab/bugsigdbr
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RoxygenNote: 7.3.2
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Encoding: UTF-8
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URL: https://waldronlab.io/bugSigSimple
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Config/testthat/edition: 3

‎tests/testthat.R‎

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# This file is part of the standard setup for testthat.
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# It is recommended that you do not modify it.
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#
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# Where should you do additional test configuration?
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# Learn more about the roles of various files in:
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# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
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# * https://testthat.r-lib.org/articles/special-files.html
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library(testthat)
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library(bugSigSimple)
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test_check("bugSigSimple")

‎tests/testthat/test-MPA.TAX.LEVELS.R‎

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#Function file: simple.R
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# Unit test: MPA.TAX.LEVELS should return the correct taxonomic level abbreviation
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library(testthat)
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test_that("MPA.TAX.LEVELS contains correct taxonomic level abbreviations", {
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expected <- c("k", "p", "c", "o", "f", "g", "s", "t")
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names(expected) <- c("kingdom", "phylum", "class", "order",

‎tests/testthat/test-countBug.R‎

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#Function file: montecarlo.R
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library(testthat)
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test_that(".countBug returns max frequency of most common taxon", {
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relevant.sigs <- list(
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sig1 = c("Bacteroides", "Escherichia"),

‎tests/testthat/test-createStudyTable.R‎

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#Function file: describe_curation.R
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bsdb <- bugsigdbr::importBugSigDB()
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test_that("createStudyTable creates a table of all studies currently in data.frame", {
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expect_s3_class(createStudyTable(bsdb[1:10,]), "data.frame")
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})

‎tests/testthat/test-createTaxonTable.R‎

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# ===== Load dependencies =====
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library(dplyr)
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library(tidyr)
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library(stringr)
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library(testthat)
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#Function file: describe_curation.R
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# ===== Mock getSignatures function =====
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getSignatures <- function(dat, tax.id.type = "metaphlan") {
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strsplit(dat$`MetaPhlAn taxon names`, "\\|")
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}
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# ===== Helper: countTaxon =====
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.countTaxon <- function(dat, x, direction = c("both", "increased", "decreased")) {
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direction <- match.arg(direction)
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if (direction != "both") {
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dat <- dplyr::filter(dat, `Abundance in Group 1` == direction)
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}
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allnames <- getSignatures(dat)
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sum(vapply(allnames, function(sig) x %in% sig, integer(1)))
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}
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# ===== Helper: Binomial Test Summary =====
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.createBinomTestSummary <- function(x, n, p = 0.5, wordy = TRUE) {
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bt <- binom.test(x, n, p)
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if (wordy) {
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paste0("p-value=", signif(bt$p.value, 2),
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" (increased freq=", x, ", total freq=", n, ")")
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} else {
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signif(bt$p.value, 2)
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}
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}
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# ===== Mock getMostFrequentTaxa function =====
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getMostFrequentTaxa <- function(dat, sig.type = "both", n = 10) {
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tab <- table(dat$`MetaPhlAn taxon names`)
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df <- as.data.frame(head(sort(tab, decreasing = TRUE), n))
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names(df) <- c("Var1", "Freq")
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df
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}
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# ===== Main Function: createTaxonTable =====
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createTaxonTable <- function(dat, n = 10) {
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dmap <- c("kingdom", "phylum", "class", "order", "family", "genus", "species")
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names(dmap) <- substring(dmap, 1, 1)
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output <- data.frame(getMostFrequentTaxa(dat, sig.type = "both", n = n),
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stringsAsFactors = FALSE) %>%
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mutate(metaphlan_name = Var1) %>%
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separate(col = Var1, sep = "\\|", into = dmap, fill = "right") %>%
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mutate(across(kingdom:species, ~ str_replace(., ".__", ""))) %>%
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rename(n_signatures = Freq)
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output <- output %>%
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mutate(n_signatures = sapply(metaphlan_name, function(x) {
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sum(grepl(x, dat$`MetaPhlAn taxon names`, fixed = TRUE))
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})) %>%
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mutate(total_signatures = sapply(metaphlan_name, function(x)
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.countTaxon(dat, x, "both"))) %>%
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mutate(increased_signatures = sapply(metaphlan_name, function(x)
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.countTaxon(dat, x, "increased"))) %>%
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mutate(decreased_signatures = sapply(metaphlan_name, function(x)
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.countTaxon(dat, x, "decreased"))) %>%
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mutate(Taxon = gsub(".+\\|", "", metaphlan_name))
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output %>%
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separate(Taxon, into = c("Taxonomic Level", "Taxon Name"), sep = "__") %>%
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mutate(`Taxonomic Level` = unname(dmap[`Taxonomic Level`])) %>%
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rowwise() %>%
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mutate(`Binomial Test pval` = .createBinomTestSummary(increased_signatures, total_signatures, wordy = FALSE)) %>%
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ungroup() %>%
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relocate(`Taxon Name`, `Taxonomic Level`, total_signatures,
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increased_signatures, decreased_signatures, `Binomial Test pval`)
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}
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# ======= TEST =========
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test_that("createTaxonTable returns correct structure", {
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mock_data <- data.frame(
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`MetaPhlAn taxon names` = c(
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"k__Bacteria|p__Firmicutes|g__Lactobacillus",
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"k__Bacteria|p__Firmicutes|g__Lactobacillus",
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"k__Bacteria|p__Bacteroidetes|g__Bacteroides"
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),
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`Abundance in Group 1` = c("increased", "decreased", "increased"),
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stringsAsFactors = FALSE
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)
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result <- createTaxonTable(mock_data, n = 2)
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expect_s3_class(result, "data.frame")
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expect_true(all(c("Taxon Name", "Taxonomic Level", "total_signatures",
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"increased_signatures", "decreased_signatures", "Binomial Test pval") %in% colnames(result)))
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expect_gt(nrow(result), 0)
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bsdb <- bugsigdbr::importBugSigDB()
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test_that("createTaxonTable creates a table of most frequent taxa in a data.frame", {
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expect_s3_class(createTaxonTable(bsdb[1:10,]), "data.frame")
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})

‎tests/testthat/test-frequencySigs.R‎

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# Mock .getTip function since it's not in global environment
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.getTip <- function(x) x
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library(testthat)
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test_that("frequencySigs identifies the most frequently occuring taxa", {
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test_sigs <- list(
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"UP_sig1" = c("Bacteroides", "Escherichia"),

‎tests/testthat/test-getCriticalN.R‎

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#Function file: montecarlo.R
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library(testthat)
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test_that("getCriticalN returns 95th percentile threshold", {
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relevant.sigs <- list(
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sig1 = c("Bacteroides", "Escherichia"),

‎tests/testthat/test-getMostFrequentTaxa.R‎

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#Function file: simple.R
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library(testthat)
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library(dplyr)
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test_that("getMostFrequentTaxa returns the most frequently occurring taxa in a table of signatures", {
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# Create test data
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test_data <- data.frame(

‎tests/testthat/test-getTip.R‎

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#Function file: simple.R
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# Unit test: .getTip should return the last part of a taxonomic string
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library(testthat)
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# Firstly, test when there are multiple levels
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test_that(".getTip returns the last part of the string", {
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s <- "k__Bacteria|p__Firmicutes|g__Lactobacillus"

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