tests/testthat/test-gs_mds.R

In federicomarini/GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

context("MDS plot of genesets works")

test_that("mds plot works", {
  p <- gs_mds(
    res_enrich = res_enrich_IFNg_vs_naive,
    res_de = res_macrophage_IFNg_vs_naive,
    annotation_obj = anno_df,
    similarity_measure = "kappa_matrix",
    mds_k = 2,
    mds_labels = 10,
    mds_colorby = "z_score"
  )
  expect_is(p, "gg")
  myset <- res_enrich_IFNg_vs_naive$gs_id[c(1, 10, 20)]
})

test_that("mds plot with specified sets works", {
  mygenesets <- res_enrich_IFNg_vs_naive$gs_id[c(1, 10, 20)]
  p <- gs_mds(
    res_enrich = res_enrich_IFNg_vs_naive,
    res_de = res_macrophage_IFNg_vs_naive,
    annotation_obj = anno_df,
    similarity_measure = "overlap_matrix",
    gs_labels = mygenesets,
    mds_colorby = "z_score",
    plot_title = "mytitle-mds"
  )
  expect_is(p, "gg")

  gtl_macrophage <- GeneTonicList(
    dds = dds_macrophage,
    res_de = res_macrophage_IFNg_vs_naive,
    res_enrich = res_enrich_IFNg_vs_naive,
    annotation_obj = anno_df
  )
  p2 <- gs_mds(
    gtl = gtl_macrophage,
    n_gs = 10
  )
  expect_is(p2, "gg")

  expect_warning(gs_mds(
    res_enrich = res_enrich_IFNg_vs_naive,
    res_de = res_macrophage_IFNg_vs_naive,
    annotation_obj = anno_df,
    gs_labels = "a_random_name",
    mds_colorby = "z_score"
  ))
})

test_that("Returning the data works as expected", {
  df <- gs_mds(
    res_enrich = res_enrich_IFNg_vs_naive[1:50, ],
    res_de = res_macrophage_IFNg_vs_naive,
    annotation_obj = anno_df,
    similarity_measure = "kappa_matrix",
    return_data = TRUE,
    mds_k = 2,
    mds_labels = 10,
    mds_colorby = "z_score"
  )
  expect_is(df, "data.frame")
  expect_true(nrow(df) == 50)
})