tests/testthat/test_utility_functions.R

In isoverse/isoorbi: Process Orbitrap Isotopocule Data

# Tests: utility functions to clean and annotate data ------------------------------------

# make both interactive test runs and auto_testing possible with a dynamic base path to the testthat folder
base_dir <- if (interactive()) file.path("tests", "testthat") else "."

context("utility functions")

# Internal utility functions =============

# factorize_dataset
test_that("factorize_dataset() tests", {

  # failure
  expect_error(factorize_dataset(),
               "argument \"dataset\" is missing, with no default")

  df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi"))

  expect_silent(factorize_dataset(df))

})

# group_if_exists
test_that("group_if_exists() tests", {

  # failure
  expect_error(group_if_exists(),
               "argument \"cols\" is missing, with no default")

  expect_error(group_if_exists(42),
               "argument \"cols\" is missing, with no default")

})

# group_by_same_groups
test_that("group_by_same_groups() tests", {

  # failure
  expect_error(group_by_same_groups(),
               "argument \"target_dataset\" is missing, with no default")

  expect_error(group_by_same_groups(42),
               "no applicable method for 'group_by' applied to an object of class \"c('double', 'numeric')\"",
               fixed = TRUE)

})

# count_grouped_distinct
test_that("count_grouped_distinct() tests", {

  # failure
  expect_error(count_grouped_distinct(),
               "argument \"dataset\" is missing, with no default")

  expect_error(count_grouped_distinct(42),
               "no applicable method for 'select' applied to an object of class \"c('double', 'numeric')\"",
               fixed = TRUE)

})

# Common utility functions to clean and annotate data ------------------------------------

# orbi_filter_satellite_peaks

test_that("orbi_filter_satellite_peaks() tests", {

  df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi"))

  expect_warning(orbi_filter_satellite_peaks(df), "deprecated")

})

# orbi_flag_satellite_peaks
test_that("orbi_flag_satellite_peaks() tests", {

  # success
  df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet_new.isox", package = "isoorbi"))

  expect_true(is.tbl(orbi_flag_satellite_peaks(orbi_simplify_isox(df))))

  # failure
  expect_error(orbi_flag_satellite_peaks(),
               "need a `dataset` data frame")

  expect_error(orbi_flag_satellite_peaks(dataset = T),
               "need a `dataset` data frame")

  expect_error(orbi_flag_satellite_peaks(dataset = df[, 1:5]),
    "`dataset` requires columns `filepath`, `filename`, `compound`, `scan.no`, `time.min`, `isotopocule`, `ions.incremental`, `tic` and `it.ms`",
    fixed = TRUE)

  df2 <- df |> mutate(dummy = 1) |> select(-scan.no)

  expect_error(orbi_flag_satellite_peaks(dataset = df2),
    "`dataset` requires columns `filepath`, `filename`, `compound`, `scan.no`, `time.min`, `isotopocule`, `ions.incremental`, `tic` and `it.ms`",
    fixed = TRUE)

})

# orbi_filter_weak_isotopocules
test_that("orbi_filter_weak_isotopocules() tests", {

  df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi"))

  expect_warning(orbi_filter_weak_isotopocules(df, min_percent = 5), "deprecated")

})


# orbi_flag_weak_isotopocules
test_that("orbi_flag_weak_isotopocules() tests", {

  # failure
  expect_error(orbi_flag_weak_isotopocules(),
               "need a `dataset` data frame",
               fixed = TRUE)

  expect_error(orbi_flag_weak_isotopocules(dataset = T),
               "need a `dataset` data frame",
               fixed = TRUE)

  df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi"))

  expect_error(orbi_flag_weak_isotopocules(dataset = df),
    "`min_percent` needs to be a single number",
    fixed = TRUE)

  expect_error(orbi_flag_weak_isotopocules(dataset = df[, 1:5]),
    "`dataset` requires columns `filepath`, `filename`, `compound`, `scan.no`, `time.min`, `isotopocule`, `ions.incremental`, `tic` and `it.ms`",
    fixed = TRUE)

  expect_error(orbi_flag_weak_isotopocules(dataset = df[0, ]),
               "`min_percent` needs to be a single number",
               fixed = TRUE)

  expect_error(orbi_flag_weak_isotopocules(dataset = df, min_percent = T),
    "`min_percent` needs to be a single number",
    fixed = TRUE)

  expect_error(orbi_flag_weak_isotopocules(dataset = df, min_percent = 100),
    "`min_percent` needs to be between 0 and 90",
    fixed = TRUE)

  expect_true(is.tbl(orbi_flag_weak_isotopocules(dataset = orbi_simplify_isox(df),
                                                   min_percent = 1)))

  df2 <-read.csv(file.path(base_dir, "test_files", "first10rows.csv")) |> select(-scan.no)

  expect_error(orbi_flag_weak_isotopocules(dataset = df2, min_percent = 1))

  df3 <- df |> mutate(
    block = as.factor("block1"),
    segment = as.factor("segment2"),
    injection = as.factor("injection3")
  )

  # success
  expect_true(is.tbl(orbi_flag_weak_isotopocules(dataset = df3, min_percent = 1)))

})

# orbi_filter_scan_intensity

test_that("orbi_filter_scan_intensity() tests", {

  df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi"))

  expect_warning(orbi_filter_scan_intensity(df, outlier_percent = 5), "deprecated")

})

# orbi_flag_outliers

test_that("orbi_flag_outliers() tests", {

  # failure

  expect_error(orbi_flag_outliers(), "need a `dataset` data frame")

  expect_error(orbi_flag_outliers(dataset = T),
               "need a `dataset` data frame",
               fixed = TRUE)

  df <- read.csv(file.path(base_dir, "test_files", "first10rows.csv"), stringsAsFactors = T)


  expect_error(orbi_flag_outliers(dataset = df),
               "need to define at least one of these parameters for identifying outliers: 'agc_window', 'agc_fold_cutoff'",
               fixed = TRUE)

  expect_error(orbi_flag_outliers(dataset = df, agc_window = T),
    "`agc_window` needs to be a vector of two numbers (low and high filter) between 0 and 100",
    fixed = TRUE)

  expect_error(orbi_flag_outliers(dataset = df, agc_window = 1000),
    "`agc_window` needs to be a vector of two numbers (low and high filter) between 0 and 100",
    fixed = TRUE)
  
  expect_error(orbi_flag_outliers(dataset = df, agc_fold_cutoff = T),
               "if provided, `agc_fold_cutoff` needs to be a single number",
               fixed = TRUE)
  
  expect_error(orbi_flag_outliers(dataset = df, agc_window = c(2,98), agc_fold_cutoff = 2),
               "can only use one method at a time, please call this function sequentially for each of these parameters: 'agc_window', 'agc_fold_cutoff'",
               fixed = TRUE)

  expect_error(orbi_flag_outliers(dataset = df[, 1:5]),
    "`dataset` requires columns `filename`, `compound`, `scan.no`, `tic` and `it.ms`",
    fixed = TRUE)

  expect_error(orbi_flag_outliers(dataset = df[0,]),
               "need to define at least one of these parameters for identifying outliers: 'agc_window', 'agc_fold_cutoff'",
               fixed = TRUE)

  df2 <- df |> mutate(dummy=1) |> select(-scan.no)
  expect_error(orbi_flag_outliers(dataset = df2, agc_window = 1),
               "`dataset` requires columns `filename`, `compound`, `scan.no`, `tic` and `it.ms`",
               fixed = TRUE)

  # success
  expect_true(is.tbl(orbi_flag_outliers(dataset = df, agc_window = c(10,90))))

  df3 <-
    orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi")) |> mutate(
      block = as.factor("block1"),
      segment = as.factor("segment2"),
      injection = as.factor("injection3")
    )

  expect_true(is.tbl(orbi_flag_outliers(dataset = df3, agc_window = c(10,90))))

})

# orbi_filter_flagged_data has been deprecated in v1.3
# test_that("orbi_filter_flagged_data() tests", {
# 
#   # failure
#   expect_error(orbi_filter_flagged_data(),
#                "need a `dataset` data frame", fixed = TRUE)
# 
#   # success
#   df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi"))
# 
#   expect_true(is.tbl(orbi_filter_flagged_data(dataset = df)))
# 
# })

# orbi_define_basepeak()

test_that("orbi_define_basepeak() tests", {

  # failure

  expect_error(orbi_define_basepeak(), "need a `dataset` data frame",
               fixed = TRUE)

  expect_error(orbi_define_basepeak(dataset = T),
               "need a `dataset` data frame",
               fixed = TRUE)

  df <- read.csv(file.path(base_dir, "test_files", "first10rows.csv"), stringsAsFactors = T)

  expect_error(orbi_define_basepeak(dataset = df),
               "`basepeak_def` needs to be a single text value identifying the isotopocule to use as the basepeak", fixed = TRUE)

  expect_error(orbi_define_basepeak(dataset = df, basepeak_def = F),
    "`basepeak_def` needs to be a single text value identifying the isotopocule to use as the basepeak", fixed = TRUE)

  expect_error(orbi_define_basepeak(dataset = df,
                                    basepeak_def = c("M0", "123")),
    "`basepeak_def` needs to be a single text value identifying the isotopocule to use as the basepeak", fixed = TRUE)

  expect_error(orbi_define_basepeak(dataset = df,
                         basepeak_def = c("ABC123")),
    "`basepeak_def` is not an isotopocule in the dataset", fixed = TRUE)


  df2 <- df |> select(-scan.no)
  expect_error(orbi_define_basepeak(dataset = df2,
                                    basepeak_def = "M0"),
    "`dataset` requires columns `filename`, `compound`, `scan.no`, `isotopocule`, and `ions.incremental`",
    fixed = TRUE)

  df3 <- df
  df3[df3 == "17O"] <- "M0"
  
  expect_error(orbi_define_basepeak(df3, basepeak_def = "M0"),
               "the M0 isotopocule exists multiple times in some scans, make sure to run orbi_flag_satellite_peaks() first",
               fixed = TRUE)
  
  df3[df3 == "M0"] <- "17O"
  
  suppressMessages(expect_error(orbi_define_basepeak(df3, basepeak_def = "M0"),
               "the 'M0' isotopocule does not exist in some scans, consider using `orbi_filter_isox()` to focus on specific file(s) and/or compound(s): \n - basepeak 'M0' is missing in 2 scans (100.0%) of compound 'HSO4-' in file 's3744'",
               fixed = TRUE))

  # success
  expect_true(is.tbl(orbi_define_basepeak(
    dataset = df, basepeak_def = "M0"
    )))

})