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## Marta R. Hidalgo
library(hipathia)
context("Load pathways")
pathways_list <- c("hsa03320", "hsa04012")
mgi <- load_pathways("hsa", pathways_list = pathways_list)
test_that("Species parameter is needed", {
expect_error(load_pathways())
})
test_that("Pathways object is a list", {
expect_is(mgi, "list")
})
test_that("Pathways object is correct", {
expect_equal(length(mgi), 7)
expect_equal(setdiff(names(mgi),
c("all.labelids", "pathigraphs", "all.genes",
"path.norm", "eff.norm", "species", "group.by")),
character(0))
expect_true(is_accepted_species(mgi$species))
expect_true(all(mgi$all.labelids[,"path.id"] %in% pathways_list))
expect_true(all(mgi$eff.norm >= 0 & mgi$eff.norm <= 1))
expect_true(all(mgi$path.norm >= 0 & mgi$path.norm <= 1))
expect_true(all(sapply(mgi$pathigraphs,
function(pg) is(pg$graph, "igraph"))))
all.effs <- unlist(sapply(mgi$pathigraphs,
function(pg) names(pg$effector.subgraphs)))
all.paths <- unlist(sapply(mgi$pathigraphs,
function(pg) names(pg$subgraphs)))
expect_true(all(all.effs == names(mgi$eff.norm)))
expect_true(all(all.paths == names(mgi$path.norm)))
expect_true(all(sapply(mgi$pathigraphs, function(pg) length(pg)) == 11))
})
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