tests/testthat/test_getPatternGeneSet.R

In CoGAPS/CoGAPS: Coordinated Gene Activity in Pattern Sets

test_that("getPatternGeneSet works on enrichment test", {
  #set up
  data(GIST)
  gs.test <- list(
    "sig_p1" = c("Hs.479754", "Hs.491582", "Hs.155591", "Hs.443625", "Hs.170355","Hs.191911"),
    "gs1" = c("Hs.2", "Hs.4", "Hs.36", "Hs.96", "Hs.202"),
    "gs2" = c("Hs.699463", "Hs.699288", "Hs.699280", "Hs.699154", "Hs.697294")
  )
  expect_no_error(getPatternGeneSet(object = GIST.result, gene.sets = gs.test, method = "enrichment"))
})

test_that("getPatternGeneSet works on overrepresentation test", {
  #set up
  data(GIST)
  gs.test <- list(
    "sig_p1" = c("Hs.479754", "Hs.491582", "Hs.155591", "Hs.443625", "Hs.170355","Hs.191911"),
    "gs1" = c("Hs.2", "Hs.4", "Hs.36", "Hs.96", "Hs.202"),
    "gs2" = c("Hs.699463", "Hs.699288", "Hs.699280", "Hs.699154", "Hs.697294")
  )
  expect_no_error(getPatternGeneSet(object = GIST.result, gene.sets = gs.test, method = "overrepresentation"))
})

test_that("plotPatternGeneSet renders a plot for enrichment test", {
  #set up
  data(GIST)
  gs.test <- list(
    "sig_p1" = c("Hs.479754", "Hs.491582", "Hs.155591", "Hs.443625", "Hs.170355","Hs.191911"),
    "gs1" = c("Hs.2", "Hs.4", "Hs.36", "Hs.96", "Hs.202"),
    "gs2" = c("Hs.699463", "Hs.699288", "Hs.699280", "Hs.699154", "Hs.697294")
  )
  gpgs_res <- getPatternGeneSet(object = GIST.result, gene.sets = gs.test, method = "enrichment")
  significant_result <- gpgs_res[[1]][gpgs_res[[1]]$gene.set == "sig_p1",]
  
  expect_true(significant_result$padj < 0.05)
  
  pl <- plotPatternGeneSet(patterngeneset = gpgs_res, whichpattern = 1, padj_threshold = 1)
  
  expect_is(pl$layers[[1]], "ggproto")
  expect_match(pl$labels$title, "Enriched gene sets in Pattern_1")
})

test_that("plotPatternGeneSet renders a plot for overrepresentation test", {
  #set up
  data(GIST)
  gs.test <- list(
    "sig_p1" = c("Hs.479754", "Hs.491582", "Hs.155591", "Hs.443625", "Hs.170355","Hs.191911"),
    "gs1" = c("Hs.2", "Hs.4", "Hs.36", "Hs.96", "Hs.202"),
    "gs2" = c("Hs.699463", "Hs.699288", "Hs.699280", "Hs.699154", "Hs.697294")
  )
  gpgs_res <- getPatternGeneSet(object = GIST.result, gene.sets = gs.test, method = "overrepresentation")
  significant_result <- gpgs_res[[1]][gpgs_res[[1]]$gene.set == "sig_p1",]
  
  expect_true(significant_result$padj < 0.05)
  
  pl <- plotPatternGeneSet(patterngeneset = gpgs_res, whichpattern = 1, padj_threshold = 1)
  
  expect_is(pl$layers[[1]], "ggproto")
  expect_match(pl$labels$title, "Overrepresented gene sets in Pattern_1")
})