tests/testthat/test-gs_heatmap.R

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

context("Testing gene set heatmap and related functionality")

test_that("Geneset heatmap is created", {
  cur_gsid <- res_enrich_IFNg_vs_naive$gs_id[1]
  p <- gs_heatmap(se = vst_macrophage,
                  res_de = res_macrophage_IFNg_vs_naive,
                  res_enrich = res_enrich_IFNg_vs_naive,
                  annotation_obj = anno_df,
                  geneset_id = cur_gsid,
                  FDR = 0.05,
                  de_only = FALSE,
                  cluster_rows = TRUE,
                  cluster_columns = TRUE,
                  center_mean = TRUE,
                  scale_row = TRUE
  )
  expect_is(p, "HeatmapList")
  p2 <- gs_heatmap(se = vst_macrophage,
                   res_de = res_macrophage_IFNg_vs_naive,
                   res_enrich = res_enrich_IFNg_vs_naive,
                   annotation_obj = anno_df,
                   geneset_id = cur_gsid,
                   FDR = 0.05,
                   de_only = TRUE,
                   cluster_rows = TRUE,
                   cluster_columns = TRUE,
                   center_mean = TRUE,
                   scale_row = TRUE
  )
  expect_is(p2, "HeatmapList")
  p3 <- gs_heatmap(se = vst_macrophage,
                   res_de = res_macrophage_IFNg_vs_naive,
                   res_enrich = res_enrich_IFNg_vs_naive,
                   annotation_obj = anno_df,
                   geneset_id = cur_gsid,
                   FDR = 0.05,
                   de_only = TRUE,
                   cluster_rows = TRUE,
                   cluster_columns = TRUE,
                   center_mean = TRUE,
                   scale_row = TRUE,
                   anno_col_info = "condition",
                   plot_title = "Just this as title"
  )
  expect_is(p3, "HeatmapList")

  # enforcing id not present in the object
  mycustomlist <- c(
    rownames(vst_macrophage)[1:10],
    "ENSmadeUPid"
  )

  expect_warning(
    p4 <- gs_heatmap(
      se = vst_macrophage,
      res_de = res_macrophage_IFNg_vs_naive,
      res_enrich = res_enrich_IFNg_vs_naive,
      annotation_obj = anno_df,
      genelist = mycustomlist,
      FDR = 0.05,
      de_only = FALSE,
      cluster_rows = TRUE,
      cluster_columns = TRUE,
      center_mean = TRUE,
      scale_row = TRUE,
      anno_col_info = "condition"
    )
  )

  file.remove("Rplots.pdf")
})