tests/testthat/test-BD_ordinations.R

In HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

test_that('Beta diversity from a list of phyloseq objects',{
  physeq_l_d = physeq_list_betaDiv(physeq_S2D2_l)
  expect_is(physeq_l_d, 'list')
  expect_equal(length(physeq_l_d), 4)
})

test_that('Beta diversity from a list of phyloseq objects (parallel)',{
  skip_on_cran()

  doParallel::registerDoParallel(2)
  physeq_l_d = physeq_list_betaDiv(physeq_S2D2_l, parallel=TRUE)
  expect_is(physeq_l_d, 'list')
  expect_equal(length(physeq_l_d), 4)
})


test_that('Make a data.frame for ordination plotting (parallel)',{
  skip_on_cran()

  # params for subseting
  doParallel::registerDoParallel(2)
  physeq_l_d = physeq_list_betaDiv(physeq_S2D2_l, parallel=TRUE)
  physeq_l_d_ord = physeq_list_ord(physeq_S2D2_l, physeq_l_d)
  physeq_l_d_ord_df = phyloseq_list_ord_dfs(physeq_S2D2_l, physeq_l_d_ord)
  expect_true('phyloseq_subset' %in% colnames(physeq_l_d_ord_df))
})



test_that('Plots created from phyloseq object',{
  skip_on_cran()

  # params for subseting
  params = get_treatment_params(physeq_S2D2, c('Substrate', 'Day'))
  expect_is(params, 'data.frame')
  expect_equal(nrow(params), 6)
  ## filtering params
  params = dplyr::filter(params, Substrate!='12C-Con')
  expect_equal(nrow(params), 4)

  # subsetting phyloseq
  ex = "(Substrate=='12C-Con' & Day=='${Day}') | (Substrate=='${Substrate}' & Day == '${Day}')"
  physeq_S2D2_l = phyloseq_subset(physeq_S2D2, params, ex)
  expect_is(physeq_S2D2_l, 'list')
  expect_equal(length(physeq_S2D2_l), 4)

  # calculating beta diversity
  physeq_S2D2_df = SIP_betaDiv_ord(physeq_S2D2_l)
  expect_is(physeq_S2D2_df, 'data.frame')
  ## plotting
  physeq_S2D2_df_p = phyloseq_ord_plot(physeq_S2D2_df)
  expect_is(physeq_S2D2_df_p, 'ggplot')

  ## alternative plot output
  physeq_S2D2_p = SIP_betaDiv_ord(physeq_S2D2_l, plot=TRUE)
  expect_is(physeq_S2D2_p, 'ggplot')
})


test_that('Plot comparing all',{
  skip_on_cran()

  # params for subseting
  params = get_treatment_params(physeq_S2D2, c('Substrate', 'Day'))
  expect_is(params, 'data.frame')
  expect_equal(nrow(params), 6)
  ## filtering params
  params = dplyr::filter(params, Substrate!='12C-Con')
  expect_equal(nrow(params), 4)

  # calculating beta diversity
  physeq_S2D2_df = SIP_betaDiv_ord(physeq_S2D2)
  expect_is(physeq_S2D2_df, 'data.frame')
  ## plotting
  physeq_S2D2_df_p = phyloseq_ord_plot(physeq_S2D2_df, point_shape='Day')
  physeq_S2D2_df_p
  expect_is(physeq_S2D2_df_p, 'ggplot')
})