Nothing
# pull data and
# return to avoid having to re-run pull_data_synapse for
# each test
testthat::expect_true(length(if (.is_connected_to_genie()) {
nsclc_data <- pull_data_synapse("NSCLC",
version = "v2.0-public"
)
cohort <- create_analytic_cohort(
data_synapse = nsclc_data$NSCLC_v2.0,
stage_dx = c("Stage IV"),
histology = "Adenocarcinoma",
regimen_drugs = "Afatinib Dimaleate",
regimen_type = "Containing"
)
plot1 <- drug_regimen_sunburst(
data_synapse = nsclc_data$NSCLC_v2.0,
data_cohort = cohort,
max_n_regimens = 4
)
} else {
nsclc_data <- list("a")
}) > 0)
test_that("Test class and length of list for sunburst plot", {
skip_if_not(genieBPC:::.is_connected_to_genie())
expect_equal(length(plot1), 2)
expect_equal(class(plot1), "list")
})
test_that("Test class and length of list for elements of sunburst data frame", {
skip_if_not(genieBPC:::.is_connected_to_genie())
expect_equal(length(plot1$treatment_history), 2)
expect_equal(
class(plot1$treatment_history),
c("tbl_df", "tbl", "data.frame")
)
})
test_that("Test class and length of list for elements
of sunburst plotly element", {
skip_if_not(genieBPC:::.is_connected_to_genie())
expect_equal(length(plot1$sunburst_plot), 8)
expect_equal(class(plot1$sunburst_plot), c("sunburst", "htmlwidget"))
})
test_that("Test something is returned", {
skip_if_not(genieBPC:::.is_connected_to_genie())
expect_error(plot1, NA)
})
test_that("Runs for all cohorts", {
skip_if_not(genieBPC:::.is_connected_to_genie())
# NSCLC
nsclc_v2_0 <- pull_data_synapse("NSCLC", "v2.0-public")
nsclc_cohort <- create_analytic_cohort(nsclc_v2_0$NSCLC_v2.0)
testthat::expect_no_error(drug_regimen_sunburst(nsclc_v2_0$NSCLC_v2.0, nsclc_cohort,
max_n_regimens = 3))
# CRC
crc_v2_0 <- pull_data_synapse("CRC", "v2.0-public")
crc_cohort <- create_analytic_cohort(crc_v2_0$CRC_v2.0)
testthat::expect_no_error(drug_regimen_sunburst(crc_v2_0$CRC_v2.0,
crc_cohort,
max_n_regimens = 3))
# BrCa
brca_v1_2 <- pull_data_synapse("BrCa", "v1.2-consortium")
brca_cohort <- create_analytic_cohort(brca_v1_2$BrCa_v1.2)
testthat::expect_no_error(drug_regimen_sunburst(brca_v1_2$BrCa_v1.2,
brca_cohort,
max_n_regimens = 3))
# PANC
panc_v1_2 <- pull_data_synapse("PANC", "v1.2-consortium")
panc_cohort <- create_analytic_cohort(panc_v1_2$PANC_v1.2)
testthat::expect_no_error(drug_regimen_sunburst(panc_v1_2$PANC_v1.2,
panc_cohort,
max_n_regimens = 3))
# Prostate
prostate_v1_2 <- pull_data_synapse(cohort = "Prostate", version = "v1.2-consortium")
prostate_cohort <- create_analytic_cohort(data_synapse = prostate_v1_2$Prostate_v1.2)
testthat::expect_no_error(drug_regimen_sunburst(prostate_v1_2$Prostate_v1.2,
prostate_cohort,
max_n_regimens = 3))
# Bladder
bladder_v1_2 <- pull_data_synapse(cohort = "BLADDER", version = "v1.2-consortium")
bladder_cohort <- create_analytic_cohort(data_synapse = bladder_v1_2$BLADDER_v1.2)
testthat::expect_no_error(drug_regimen_sunburst(bladder_v1_2$BLADDER_v1.2,
bladder_cohort,
max_n_regimens = 3))
})
test_that("data_synapse parameter", {
# missing the data_synapse input parameter
expect_error(drug_regimen_sunburst())
# data_synapse input parameter isn't a list
expect_error(drug_regimen_sunburst(data_synapse = "a"))
# data_synapse parameter is a list, but isn't the right list
expect_error(drug_regimen_sunburst(data_synapse = list("a" = "a",
"b" = "b"),
data_cohort = nsclc_data))
})
test_that("data_cohort parameter", {
# missing data_cohort parameter
expect_error(drug_regimen_sunburst(data_synapse = nsclc_data))
# data_cohort parameter isn't a list
expect_error(drug_regimen_sunburst(
data_synapse = nsclc_data,
data_cohort = "a"
))
# data_cohort parameter is a list, but isn't the right list
expect_error(drug_regimen_sunburst(
data_synapse = nsclc_data$NSCLC_v2.0,
data_cohort = list("a", "b")
))
})
test_that("lines of tx specified", {
skip_if_not(genieBPC:::.is_connected_to_genie())
# line of therapy isn't specified, select all
test1a <- drug_regimen_sunburst(
data_synapse = nsclc_data$NSCLC_v2.0,
data_cohort = cohort
)
# compare to manually inputting the max number
max_n <- left_join(cohort$cohort_ca_dx,
nsclc_data$NSCLC_v2.0$ca_drugs,
by = c("cohort", "record_id", "ca_seq"),
multiple = "all"
) %>%
drop_na(regimen_drugs) %>%
count(record_id) %>%
summarize(n_reg = max(n)) %>%
pull(n_reg)
test1b <- drug_regimen_sunburst(
data_synapse = nsclc_data$NSCLC_v2.0,
data_cohort = cohort,
max_n_regimens = max_n
)
expect_equal(test1a, test1b)
})
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