tests/testthat/test-happy_hour.R

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

context("The happy hour is running!")

# test_that("The happy hour starts", {
#   my_html_report <- happy_hour(
#     dds = dds_macrophage,
#     res_de = res_macrophage_IFNg_vs_naive,
#     res_enrich = res_enrich_IFNg_vs_naive,
#     annotation_obj = anno_df,
#     project_id = "testsuite",
#     mygenesets = res_enrich_IFNg_vs_naive$gs_id[2:3],
#     mygenes = deseqresult2df(res_de)$id[1:5],
#     output_file = "test.html",
#     force_overwrite = FALSE,
#     open_after_creating = FALSE
#   )
#   expect_is(my_html_report, "character")
#   file.remove("test.html")
#   # my_pdf_report <- happy_hour(
#   #   dds = dds_macrophage,
#   #   res_de = res_macrophage_IFNg_vs_naive,
#   #   res_enrich = res_enrich_IFNg_vs_naive,
#   #   annotation_obj = anno_df,
#   #   project_id = "testsuite",
#   #   mygenesets = res_enrich_IFNg_vs_naive$gs_id[1:2],
#   #   mygenes = deseqresult2df(res_de)$id[1:5],
#   #   output_file = "test.pdf",
#   #   force_overwrite = FALSE,
#   #   open_after_creating = FALSE
#   # )
#   # expect_is(my_pdf_report, "character")
#   # file.remove("test.pdf")
# })

# test_that("Errors and warnings are thrown", {
#   expect_error(
#     happy_hour(
#       dds = dds_macrophage,
#       res_de = res_macrophage_IFNg_vs_naive,
#       res_enrich = res_enrich_IFNg_vs_naive,
#       annotation_obj = anno_df,
#       project_id = "testsuite",
#       mygenesets = res_enrich_IFNg_vs_naive$gs_id[1:2],
#       mygenes = deseqresult2df(res_de)$id[1:5],
#       output_file = "doc1.html",
#       output_format = "pdf_document",
#       force_overwrite = TRUE,
#       open_after_creating = FALSE
#     )
#   )
#   expect_error(
#     happy_hour(
#       dds = dds_macrophage,
#       res_de = res_macrophage_IFNg_vs_naive,
#       res_enrich = res_enrich_IFNg_vs_naive,
#       annotation_obj = anno_df,
#       project_id = "testsuite",
#       mygenesets = res_enrich_IFNg_vs_naive$gs_id[1:2],
#       mygenes = deseqresult2df(res_de)$id[1:5],
#       output_file = "doc1.ppt",
#       output_format = "powerpoint_presentation",
#       force_overwrite = TRUE,
#       open_after_creating = FALSE
#     )
#   )
#
#   file.create("decoy.html")
#   expect_warning(
#     happy_hour(
#       dds = dds_macrophage,
#       res_de = res_macrophage_IFNg_vs_naive,
#       res_enrich = res_enrich_IFNg_vs_naive,
#       annotation_obj = anno_df,
#       project_id = "testsuite",
#       mygenesets = res_enrich_IFNg_vs_naive$gs_id[5:6],
#       mygenes = deseqresult2df(res_de)$id[1:5],
#       output_file = "decoy.html",
#       force_overwrite = TRUE,
#       open_after_creating = FALSE
#     )
#   )
#   expect_error(
#     happy_hour(
#       dds = dds_macrophage,
#       res_de = res_macrophage_IFNg_vs_naive,
#       res_enrich = res_enrich_IFNg_vs_naive,
#       annotation_obj = anno_df,
#       project_id = "testsuite",
#       mygenesets = res_enrich_IFNg_vs_naive$gs_id[1:4],
#       mygenes = deseqresult2df(res_de)$id[1:5],
#       output_file = "decoy.html",
#       force_overwrite = FALSE,
#       open_after_creating = FALSE
#     )
#   )
#   file.remove("decoy.html")
#
#   file.create("custom.Rmd")
#   expect_error(
#     happy_hour(
#       dds = dds_macrophage,
#       res_de = res_macrophage_IFNg_vs_naive,
#       res_enrich = res_enrich_IFNg_vs_naive,
#       annotation_obj = anno_df,
#       project_id = "testsuite",
#       mygenesets = res_enrich_IFNg_vs_naive$gs_id[3:4],
#       mygenes = deseqresult2df(res_de)$id[1:5],
#       input_rmd = "custom.Rmd",
#       output_file = "custom.html",
#       force_overwrite = TRUE,
#       open_after_creating = FALSE
#     )
#   )
#   expect_error(
#     happy_hour(
#       dds = dds_macrophage,
#       res_de = res_macrophage_IFNg_vs_naive,
#       res_enrich = res_enrich_IFNg_vs_naive,
#       annotation_obj = anno_df,
#       project_id = "testsuite",
#       mygenesets = res_enrich_IFNg_vs_naive$gs_id[1:2],
#       mygenes = deseqresult2df(res_de)$id[1:5],
#       input_rmd = "custom2.Rmd",
#       output_file = "custom.html",
#       force_overwrite = TRUE,
#       open_after_creating = FALSE
#     )
#   )
#   file.remove("custom.Rmd")
# })