tests/testthat/test_plotting_functions.R

In isoverse/isoorbi: Process Orbitrap Isotopocule Data

context("plotting functions")

# filter_isotopocules

test_that("filter_isotopocules() tests", {
  
  # failure
  expect_error(filter_isotopocules(),
               "argument \"dataset\" is missing, with no default",
               fixed = TRUE)
  
  df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi")) |>
    orbi_simplify_isox()
  
  expect_error(filter_isotopocules(df),
               "argument \"isotopocules\" is missing, with no default",
               fixed = TRUE)
  
  suppressWarnings(expect_error(filter_isotopocules(df, isotopocules = "M0"),
               "none of the provided `isotopocules` are in the dataset",
               fixed = TRUE))
  
  # success
  expect_true(is.tbl(filter_isotopocules(df, isotopocules = "17O")))
  
})

# dynamic_y_scale

test_that("dynamic_y_scale() tests", {
  
  # failure
  expect_error(dynamic_y_scale(),
               "argument \"plot\" is missing, with no default",
               fixed = TRUE)
  
  df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi")) |>
    orbi_simplify_isox() |> orbi_define_basepeak(basepeak_def = "15N") |>
    orbi_analyze_shot_noise()
  
})

# orbi_get_isotopocule_coverage

test_that("orbi_get_isotopocule_coverage() tests", {
  
  # failure
  expect_error(orbi_get_isotopocule_coverage(),
               "need a `dataset` data frame",
               fixed = TRUE)
  
  # success
  
  df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi")) |>
    orbi_simplify_isox()
  
  dataset <- df |> factorize_dataset(c("filename", "compound", "isotopocule"))
  
  expect_true(is.tbl(orbi_get_isotopocule_coverage(dataset)))
  
})

# orbi_plot_satellite_peaks 

test_that("orbi_plot_satellite_peaks() tests", {
  
  # failure
  expect_error(orbi_plot_satellite_peaks(),
               "need a `dataset` data frame",
               fixed = TRUE)
  
  df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi")) |>
    orbi_simplify_isox()
  
  expect_error(orbi_plot_satellite_peaks(df),
               "`dataset` requires column `is_satellite_peak` - make sure to run `orbi_flag_satellite_peaks()` first",
               fixed = TRUE)
  
  # success
  df2 <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi")) |>
    orbi_simplify_isox() |> orbi_flag_satellite_peaks()
  
  library(ggplot2)
  expect_type(orbi_plot_satellite_peaks(df2), "list")
  
})

# orbi_plot_raw_data 

test_that("orbi_plot_raw_data() tests", {
  
  # failure
  expect_error(orbi_plot_raw_data(),
               "need a `dataset` data frame",
               fixed = TRUE)
  
  df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi")) |>
    orbi_simplify_isox() |> orbi_flag_outliers(agc_fold_cutoff = 2)
  
  expect_error(orbi_plot_raw_data(df),
               "`y` has to be provided, can be any expression valid in the data frame, common examples include intensity, ratio, tic * it.ms",
               fixed = TRUE)
  
  # success
  
  library(ggplot2)
  expect_type(orbi_plot_raw_data(df, y = "ratio"), "list")
  
  df2 <- orbi_read_isox(system.file("extdata", "testfile_flow.isox", package = "isoorbi")) |>
    orbi_simplify_isox() |> orbi_flag_outliers(agc_fold_cutoff = 2)
  
  fig2 <- orbi_plot_raw_data(df2, y = "ratio", show_outliers = TRUE)
  
  expect_equal(length(fig2$layers), 1)
  
})

# orbi_plot_isotopocule_coverage 

test_that("orbi_plot_isotopocule_coverage() tests", {
  
  # failure
  expect_error(orbi_plot_isotopocule_coverage(),
               "need a `dataset` data frame",
               fixed = TRUE)
  
  df <- orbi_read_isox(system.file("extdata", "testfile_dual_inlet.isox", package = "isoorbi")) |>
    orbi_simplify_isox()
  
  expect_error(orbi_plot_isotopocule_coverage(df, isotopocules = 42),
               "`isotopocules` has to be a character vector if provided",
               fixed = TRUE)
  
  # success
  
  library(ggplot2)
  fig <- orbi_plot_isotopocule_coverage(df)
  
  expect_type(fig, "list")
  
  expect_equal(fig$facet$vars(), character(0))
  
})