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Modifed all tests. Removed file path and load peakCombinder associate…
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…d data set. Check all tests for the new used data.
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@MarkusMuck
MarkusMuck committed Jul 18, 2024
1 parent dd0abd9 commit 3bf4873
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3 changes: 2 additions & 1 deletion tests/testthat.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,4 +9,5 @@
library(testthat)
library(peakCombiner)

testthat::test_check("peakCombiner")
#testthat::test_check(package = "peakCombiner")
testthat::test_package(package = "peakCombiner")
138 changes: 61 additions & 77 deletions tests/testthat/test-center_expand_regions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -19,65 +19,69 @@ input_colnames_pre <- c(
)
input_colnames_post <- c(
"chrom", "start", "end", "name", "score", "strand",
"center", "sample_name", "center_origin", "input_names"
"center", "sample_name", "input_names"
)
output_colnames_pre <- c(
"chrom", "start", "end", "name", "score", "strand",
"center", "sample_name"
)
output_colnames_post <- c(
"chrom", "start", "end", "name", "score", "strand",
"center", "sample_name", "center_origin", "input_names"
"center", "sample_name", "input_names"
)
##
test_data <- readr::read_tsv("lists/synthetic_genomic_regions.bed", show_col_types = FALSE)
#test_data <- readr::read_tsv("data-raw/synthetic_data.bed", show_col_types = FALSE)
test_data <- peakCombiner::syn_sample_sheet
##
test_data_prepared <- prepare_input_regions(
data = test_data
)
##
test_data_center_expand <- center_expand_regions(
data = test_data_prepared,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
)
restult_colnames <- colnames(test_data_center_expand)
##
test_data_filtered <- filter_regions(
data = test_data_center_expand,
filter_by_blacklist = "hg38", # "hg38",
filter_by_chromosome_names = NULL,
filter_by_significance = NULL,
filter_by_top_enriched = NULL
) |> suppressWarnings()
exclude_by_blacklist = "hg38", # "hg38",
include_by_chromosome_name = NULL,
include_above_score_cutoff = NULL,
include_top_n_scoring = NULL,
show_messages = TRUE
)
##
test_data_combined <- combine_regions(
data = test_data_filtered,
found_in_samples = 2,
center = "nearest"
combined_center = "nearest",
annotate_with_input_names = TRUE,
combined_sample_name = "combined"
)
##
test_data_combined_ce <- center_expand_regions(
data = test_data_combined,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
)
### -----------------------------------------------------------------------###
### Test input
### -----------------------------------------------------------------------###

test_that("Test if function works with pre-combined input", {
expect_no_error(center_expand_regions(
testthat::test_that("Test if function works with pre-combined input", {
testthat::expect_no_error(center_expand_regions(
data = test_data_prepared,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
))
})

test_that("Test if function works with post-combined input", {
expect_no_error(center_expand_regions(
testthat::test_that("Test if function works with post-combined input", {
testthat::expect_no_error(center_expand_regions(
data = test_data_combined,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
))
})
Expand All @@ -98,14 +102,14 @@ test_that("Required input data has the expected structure", {
expect_true(is.character(data$strand))
expect_true(is.numeric(data$center))
expect_true(is.character(data$sample_name))
expect_true(sum(str_detect(data$name, "|")) > 0)
expect_true(sum(stringr::str_detect(data$name, "|")) > 0)
})

test_that("Required input data has the expected structure", {

data <- test_data_combined

expect_equal(length(names(data)), 10)
expect_equal(length(names(data)), 9)
expect_identical(names(data), input_colnames_post)
expect_true(is.character(data$chrom))
expect_true(is.numeric(data$start))
Expand All @@ -114,21 +118,20 @@ test_that("Required input data has the expected structure", {
expect_true(is.numeric(data$score))
expect_true(is.character(data$strand))
expect_true(is.numeric(data$center))
expect_true(is.character(data$center_origin))
expect_true(sum(str_detect(data$input_names, "|")) > 0)
expect_true(sum(stringr::str_detect(data$input_names, "|")) > 0)
})

### -----------------------------------------------------------------------###

test_that("Required paramter 'center_by' has the expected structure/value", {
expect_no_error(center_expand_regions(
data = test_data_prepared,
center_by = "coluMn_value",
center_by = "center_Column",
expand_by = NULL
))
expect_error(center_expand_regions(
data = test_data_prepared,
center_by = c("column_value", "calculated_value"),
center_by = c("center_column", "calculated_value"),
expand_by = NULL
), "center_by")
expect_error(center_expand_regions(
Expand All @@ -150,28 +153,28 @@ test_that("Required paramter 'center_by' has the expected structure/value", {

### -----------------------------------------------------------------------###

test_that("Required paramter expand_by has the expected structure/value", {
expect_no_error(center_expand_regions(
testthat::test_that("Required paramter expand_by has the expected structure/value", {
testthat::expect_no_error(center_expand_regions(
data = test_data_prepared,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
))
expect_error(center_expand_regions(
testthat::expect_error(center_expand_regions(
data = test_data_prepared,
center_by = "column_value",
expand_by = NA
), )
expect_error(center_expand_regions(
),)
testthat::expect_error(center_expand_regions(
data = test_data_prepared,
center_by = "column_value",
expand_by = c(1, 2, 3)
), )
expect_error(center_expand_regions(
),)
testthat::expect_error(center_expand_regions(
data = test_data_prepared,
center_by = "column_value",
expand_by = "nonexisting"
), )
})
),)
devtools::document()})

### -----------------------------------------------------------------------###
### Test Output
Expand All @@ -195,17 +198,17 @@ test_that("Output data frame is correct for pre-combined", {
expect_true(is.numeric(data$center))
expect_true(is.character(data$sample_name))

expect_equal(mean(data$center), 1942.2535)
expect_identical(nrow(data), as.integer(71))
expect_identical(data$start[1], 250)
expect_equal(mean(data$center), 2452.92308)
expect_identical(nrow(data), as.integer(52))
expect_identical(data$start[1], 352)
})

test_that("Output data frame is correct for post-combined", {

data <- test_data_combined_ce

expect_setequal(colnames(data), output_colnames_post)
expect_equal(ncol(data), 10)
expect_equal(ncol(data), 9)

expect_identical(class(data)[2], "tbl")

Expand All @@ -216,107 +219,88 @@ test_that("Output data frame is correct for post-combined", {
expect_true(is.numeric(data$score))
expect_true(is.character(data$strand))
expect_true(is.numeric(data$center))
expect_true(is.character(data$center_origin))

expect_equal(mean(data$center), 2192.3077)
expect_identical(nrow(data), as.integer(13))
expect_identical(data$start[1], 100)
expect_identical(data$end[1], 900)
expect_identical(data$end[1], 900)
expect_equal(mean(data$center), 2711)
expect_identical(nrow(data), as.integer(10))
expect_identical(data$start[1], 152)
expect_identical(data$end[1], 850)
expect_identical(data$end[1], 850)
})

test_that("Output data frame is correct for data_prepared", {
##
data <- test_data_prepared
result <- center_expand_regions(
data = data,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
)
##
expect_no_error(center_expand_regions(
data = data,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
))
##
expect_identical(nrow(result), 71L)
expect_identical(result$start[9], as.numeric(250))
expect_identical(nrow(result), 52L)
expect_identical(result$start[9], as.numeric(252))
})
##
test_that("Output data frame is correct for data_center_expand", {
##
data <- test_data_center_expand
result <- center_expand_regions(
data = data,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
)
##
expect_no_error(center_expand_regions(
data = data,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
))
##
expect_identical(nrow(result), 71L)
expect_identical(result$start[9], as.numeric(250))
expect_identical(nrow(result), 52L)
expect_identical(result$start[9], as.numeric(252))
})
##
test_that("Output data frame is correct for data_filtered", {
##
data <- test_data_filtered
result <- center_expand_regions(
data = data,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
)
##
expect_no_error(center_expand_regions(
data = data,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
))
##
expect_identical(nrow(result), 71L)
expect_identical(result$start[9], as.numeric(250))
expect_identical(nrow(result), 52L)
expect_identical(result$start[9], as.numeric(252))
})
##
test_that("Output data frame is correct for data_combined", {
##
data <- test_data_combined
result <- center_expand_regions(
data = data,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
)
##
expect_no_error(center_expand_regions(
data = data,
center_by = "column_value",
center_by = "center_column",
expand_by = NULL
))
##
expect_identical(nrow(result), 13L)
expect_identical(result$start[9], as.numeric(100))
expect_identical(nrow(result), 10L)
expect_identical(result$start[9], as.numeric(252))
})
##
### -----------------------------------------------------------------------###
##
test_that("All newly center and expand regions do have only positive values", {
##
data_input <- readr::read_tsv(paste0("lists/input_data-bed3.bed"))
prep_data <- prepare_input_regions(data = data_input,score_colname = NULL)
##
expect_no_error(center_expand_regions(
data = prep_data,
center_by = "column_value",
expand_by = NULL
))
##
expect_message(center_expand_regions(
data = prep_data,
center_by = "column_value",
expand_by = 500
))
})
68 changes: 0 additions & 68 deletions tests/testthat/test-collapse_summits.R
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