tests/testthat/test-enhance_tables.R

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

context("Testing enhance_tables and related functionality")

test_that("Enhanced table is created", {
  p <- enhance_table(res_enrich_IFNg_vs_naive,
                     res_macrophage_IFNg_vs_naive,
                     annotation_obj = anno_df,
                     n_gs = 50,
                     chars_limit = 60)
  expect_is(p, "gg")

  pl <- ggplotly(p)
  expect_is(pl, "plotly")
  expect_is(pl, "htmlwidget")

  p2 <- enhance_table(res_enrich_IFNg_vs_naive,
                      res_macrophage_IFNg_vs_naive,
                      annotation_obj = anno_df,
                      n_gs = 5,
                      chars_limit = 60,
                      plot_title = "My custom title")
  expect_is(p2, "gg")


})

test_that("The distillery is up and running", {
  d_en <- distill_enrichment(res_enrich_IFNg_vs_naive,
                             res_macrophage_IFNg_vs_naive,
                             annotation_obj = anno_df,
                             n_gs = 100,
                             cluster_fun = "cluster_markov")
  
  expect_is(d_en, "list")
  expect_is(d_en$distilled_table, "data.frame")
  expect_is(d_en$distilled_em, "igraph")
  
  library("igraph")
  
  d_en_louvain <- distill_enrichment(res_enrich_IFNg_vs_naive,
                                     res_macrophage_IFNg_vs_naive,
                                     annotation_obj = anno_df,
                                     n_gs = 100,
                                     cluster_fun = "cluster_louvain")
  
  d_en_walktrap <- distill_enrichment(res_enrich_IFNg_vs_naive,
                                     res_macrophage_IFNg_vs_naive,
                                     annotation_obj = anno_df,
                                     n_gs = 100,
                                     cluster_fun = "cluster_walktrap")
  
  expect_error(distill_enrichment(res_enrich_IFNg_vs_naive,
                                  res_macrophage_IFNg_vs_naive,
                                  annotation_obj = anno_df,
                                  n_gs = 100,
                                  cluster_fun = "cluster_wrong_function"))
})