tests/testthat/test-plot_orthotree.R

In neurogenomics/orthogene: Interspecies gene mapping

test_that("plot_orthotree works", {
    
  if(require("ape")){
      species <- c("human","monkey","mouse")
      ### homologene ####
      orthotree_hg <- plot_orthotree(species = species, 
                                     method = "homologene")
      ### babelgene ####
      orthotree_bg <- plot_orthotree(species = species, 
                                     # save_paths = c("~/Desktop/ggtree.pdf",
                                     #                "~/Desktop/ggtree.png")
                                     method = "babelgene")
      #### gprofiler ####
      ## Omitting this test because it takes a verrrry long time
      # orthotree_gp <- orthogene::plot_orthotree(species = species,
      #                                           method = "gprofiler")
      
      for(orthotree in list(orthotree_hg, orthotree_bg)){ 
          testthat::expect_true(
              all(c("plot","tree","orth_report","metadata") %in% names(orthotree))
          )
          testthat::expect_true(methods::is(orthotree$plot,"gg"))
          testthat::expect_true(methods::is(orthotree$tree,"phylo"))
          testthat::expect_true(methods::is(orthotree$orth_report,"data.frame"))
          testthat::expect_true(methods::is(orthotree$metadata,"data.frame"))
          testthat::expect_true(methods::is(orthotree$clades,"data.frame"))
          testthat::expect_equal(length(species), length(orthotree$tree$tip.label))
          testthat::expect_equal(sort(unname(orthotree$tree$tip.label)),
                                 sort(c("homo sapiens","macaca mulatta","mus musculus")))
      } 
  }
  
})