tests/testthat/test-user-special.R

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

# LIBS
library(phylotaR)
library(testthat)

# DATA
wd <- tempdir()
ps <- parameters(wd = wd)
phylota <- phylotaR:::random_phylota()

# RUNNING
context("Testing 'user-special'")
phylotaR:::cleanup(wd)
test_that("read_phylota() works", {
  # setup clstrs_sqs
  phylotaR:::cache_setup(ps)
  phylotaR:::obj_save(
    wd = ps[["wd"]], nm = "clstrs_sqs",
    obj = list(
      "clstrs" = phylota@clstrs,
      "sqs" = phylota@sqs
    )
  )
  phylotaR:::obj_save(wd = ps[["wd"]], obj = phylota@txdct, nm = "txdct")
  res <- read_phylota(wd = ps[["wd"]])
  expect_true(inherits(res, "Phylota"))
})
phylotaR:::cleanup(wd)
test_that("write_sqs() works", {
  cid <- sample(phylota@cids, 1)
  sids <- phylota@clstrs@clstrs[[cid]]@sids
  n <- ifelse(length(sids) > 50, 50, length(sids))
  sids <- sample(sids, n)
  write_sqs(
    phylota = phylota, outfile = file.path(wd, "test.fasta"),
    sid = sids, sq_nm = "myfavouritegene"
  )
  expect_true(file.exists(file.path(wd, "test.fasta")))
})
phylotaR:::cleanup(wd)
test_that("plot_phylota_treemap() works", {
  n <- ifelse(length(phylota@cids) > 5, 5, length(phylota@cids))
  cids <- phylota@cids[1:n]
  area <- sample(c("ntx", "nsq"), 1)
  fill <- sample(c("NULL", "typ", "ntx", "nsq"), 1)
  p1 <- plot_phylota_treemap(
    phylota = phylota, cids = cids, area = area,
    fill = fill
  )
  p1
  expect_true(inherits(p1, "gg"))
  n <- ifelse(length(phylota@txids) > 5, 5, length(phylota@txids))
  txids <- phylota@txids[1:n]
  area <- sample(c("ncl", "nsq"), 1)
  fill <- sample(c("NULL", "nsq", "ncl"), 1)
  p2 <- plot_phylota_treemap(
    phylota = phylota, txids = txids, area = area,
    fill = fill
  )
  p2
  expect_true(inherits(p2, "gg"))
})
test_that("plot_phylota_pa() works", {
  n <- ifelse(length(phylota@cids) > 10, 10, length(phylota@cids))
  cids <- phylota@cids[1:n]
  spp <- unique(get_txids(
    phylota = phylota, txids = phylota@txids,
    rnk = "species"
  ))
  spp <- spp[spp != ""]
  p <- plot_phylota_pa(phylota = phylota, cids = cids, txids = spp)
  expect_true(inherits(p, "gg"))
})
test_that("mk_txid_in_sq_mtrx() works", {
  n <- ifelse(length(phylota@sids) > 50, 50, length(phylota@sids))
  sids <- sample(phylota@sids, n)
  n <- ifelse(length(phylota@txids) > 10, 10, length(phylota@txids))
  txids <- sample(phylota@txids, n)
  res <- phylotaR:::mk_txid_in_sq_mtrx(
    phylota = phylota, txids = txids,
    sids = sids
  )
  expect_true(inherits(res, "matrix"))
  sid <- sample(colnames(res), 1)
  txid <- sample(rownames(res), 1)
  ads <- phylotaR:::descendants_get(
    id = txid, txdct = phylota@txdct,
    direct = FALSE
  )
  all_ids <- c(ads, txid)
  sq <- phylota@sqs@sqs[[which(phylota@sqs@ids == sid)]]
  expect_true(res[txid, sid] == (sq@txid %in% all_ids))
})
test_that("is_txid_in_sq() works", {
  txid <- sample(phylota@txids, 1)
  sid <- sample(phylota@sids, 1)
  res <- is_txid_in_sq(phylota = phylota, txid = txid, sid = sid)
  expect_true(inherits(res, "logical"))
})
test_that("is_txid_in_clstr() works", {
  txid <- sample(phylota@txids, 1)
  cid <- sample(phylota@cids, 1)
  res <- is_txid_in_clstr(phylota = phylota, txid = txid, cid = cid)
  expect_true(inherits(res, "logical"))
})
test_that("summary_phylota() works", {
  test_phylota <- phylota
  n <- ifelse(length(phylota@cids) > 3, 3, length(phylota@cids))
  cids <- sample(phylota@cids, n)
  test_phylota <- drop_clstrs(phylota = test_phylota, cid = cids)
  res <- phylotaR:::summary_phylota(test_phylota)
  expect_true(inherits(res, "data.frame"))
})
test_that("update_phylota() works", {
  test_phylota <- phylota
  n <- ifelse(length(phylota@cids) > 10, 10, length(phylota@cids))
  cltrrecs <- sample(test_phylota@clstrs@clstrs, n)
  test_phylota@clstrs <- phylotaR:::clstrarc_gen(clstrrecs = cltrrecs)
  expect_true(length(test_phylota@cids) == length(phylota@cids))
  test_phylota <- phylotaR:::update_phylota(test_phylota)
  expect_false(length(test_phylota@cids) == length(phylota@cids))
  expect_true(length(test_phylota@cids) == 10)
})