Nothing
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')
})
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