context("cyto_gatingTemplate-helpers")
# MISSING TESTS
# CYTO_GATINGTEMPLATE_EDIT
# CYTO_GATINGTEMPLATE_APPLY
# cyto_gatingTemplate_select/active --------------------------------------------
test_that("cyto_gatingTemplate_select", {
cyto_gatingTemplate_select("Activation")
expect_equal(getOption("CytoExploreR_gatingTemplate"),
"Activation.csv")
cyto_gatingTemplate_select("Activation_gatingTemplate.csv")
expect_equal(getOption("CytoExploreR_gatingTemplate"),
"Activation_gatingTemplate.csv")
expect_equal(cyto_gatingTemplate_active(),
"Activation_gatingTemplate.csv")
})
# cyto_gatingTemplate_create ---------------------------------------------------
test_that("cyto_gatingTemplate_create", {
cyto_gatingTemplate_create("New-gatingTemplate.csv")
new_gt <- read.csv("New-gatingTemplate.csv", header = TRUE)
expect_equal(colnames(new_gt), c("alias",
"pop",
"parent",
"dims",
"gating_method",
"gating_args",
"collapseDataForGating",
"groupBy",
"preprocessing_method",
"preprocessing_args"))
})
# cyto_gatingTemplate_update --------------------------------------------------
test_that("cyto_gatingTemplate_update", {
# UPDATE CYTORSUITE GATINGTEMPLATE
cyto_gatingTemplate_update("Ref-old-gatingTemplate.csv")
expect_equal(read.csv("Updated-gatingTemplate.csv", header =TRUE),
read.csv("Ref-updated-gatingTemplate.csv", header = TRUE))
})
# .cyto_gatingTemplate_check ---------------------------------------------------
test_that(".cyto_gatingTemplate_check", {
# BYPASS CHECKS
expect_equal(.cyto_gatingTemplate_check(parent = "T Cells",
alias = "CD4 T Cells",
"NOTINWD.csv"),
NULL)
# ENTRY EXISTS ALREADY
expect_error(.cyto_gatingTemplate_check(parent = "T Cells",
alias = "CD4 T Cells",
"Reference-Activation-gatingTemplate.csv"),
"Supply another gatingTemplate or edit gate(s) using cyto_gate_edit.",
fixed = TRUE)
})
unlink("Updated-gatingTemplate.csv")
unlink("New-gatingTemplate.csv")
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