tests/testthat/test-enrichment_map.R

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

context("Testing enrichmentmap and related functionality")

test_that("Graph is generated", {
  g <- enrichment_map(res_enrich = res_enrich_IFNg_vs_naive,
                      res_de = res_macrophage_IFNg_vs_naive,
                      annotation_obj = anno_df,
                      n_gs = 50)
  expect_is(g, "igraph")

  res_enrich_withscores <- get_aggrscores(res_enrich_IFNg_vs_naive,
                                          res_macrophage_IFNg_vs_naive,
                                          annotation_obj = anno_df,
                                          aggrfun = mean)
  g2 <- enrichment_map(res_enrich = res_enrich_withscores,
                      res_de = res_macrophage_IFNg_vs_naive,
                      annotation_obj = anno_df,
                      color_by = "z_score",
                      n_gs = 50)
  expect_is(g2, "igraph")

  res_pos_z <- res_enrich_withscores[res_enrich_withscores$z_score >= 0, ]
  g3 <- enrichment_map(res_enrich = res_pos_z,
                       res_de = res_macrophage_IFNg_vs_naive,
                       annotation_obj = anno_df,
                       color_by = "z_score",
                       n_gs = 50)
  expect_is(g3, "igraph")


  library(magrittr)
  vi <- visNetwork::visIgraph(g) %>%
    visOptions(highlightNearest = list(enabled = TRUE,
                                       degree = 1,
                                       hover = TRUE),
               nodesIdSelection = TRUE)

  expect_is(vi, "visNetwork")
  expect_is(vi, "htmlwidget")
})

test_that("Errors and warnings are thrown", {
  expect_error(
    enrichment_map(res_enrich = res_enrich_IFNg_vs_naive,
                   res_de = res_macrophage_IFNg_vs_naive,
                   annotation_obj = anno_df,
                   color_by = "pvalue",
                   n_gs = 50)
  )
})