tests/testthat/test-create-report.R

In martahidalgo/hipathia: HiPathia: High-throughput Pathway Analysis

#
# ## Marta R. Hidalgo
#
# library(hipathia)
# context("Create report")
#
# data("brca")
# data("comp")
# data(results)
# extdata_folder <- system.file("extdata", package = "hipathia")
# output_folder <- paste0(extdata_folder, "/save_noColors")
# mgi <- load_pathways("hsa", pathways_list = c("hsa03320", "hsa04012"))
# sample_group <- colData(brca)[,1]
# colors_de <- node_color_per_de(results, mgi, sample_group, "Tumor", "Normal")
# create_report(results, comp, mgi, output_folder)
#
# test_that("Folders are created", {
#     expect_true(file.exists(paste0(output.folder, "/pathway-viewer")))
#     expect_true(file.exists(paste0(output.folder, "/pathway-viewer/conf")))
#     expect_true(file.exists(paste0(output.folder, "/pathway-viewer/css")))
#     expect_true(file.exists(paste0(output.folder,
#                                    "/pathway-viewer/fontawesome")))
#     expect_true(file.exists(paste0(output.folder, "/pathway-viewer/fonts")))
#     expect_true(file.exists(paste0(output.folder,
#                                    "/pathway-viewer/normalize-css")))
#     expect_true(file.exists(paste0(output.folder, "/pathway-viewer/pathways")))
#     expect_true(file.exists(paste0(output.folder,
#                                    "/pathway-viewer/webcomponentsjs")))
#     expect_true(file.exists(paste0(output.folder,
#                                    "/pathway-viewer/index.html")))
#     expect_true(file.exists(paste0(output.folder,
#                                    "/pathway-viewer/pathway-viewer.html")))
#     expect_true(file.exists(paste0(output.folder,
#                                    "/pathway-viewer/report_legend.png")))
#     expect_true(file.exists(paste0(output.folder,
#                                    "/pathway-viewer/report_logo.png")))
#     expect_true(file.exists(paste0(output.folder,
#                                    "/pathway-viewer/report_title.png")))
# })
#
# test_that("All pathway files have been created", {
#     expect_equal(length(list.files(paste0(output.folder,
#                                           "/pathway-viewer/pathways"))),
#                  3 * length(mgi$pathigraphs) + 1)
# })
#