tests/testthat/test-utility_funcs.R

In proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics

context("utility_funcs")

test_that("check_sample_consistency", {
  #TODO: check if the warnings are raised expect_warning
  
  df_test = check_sample_consistency(sample_annotation = example_sample_annotation, 
                                     df_long = example_proteome, 
                                     sample_id_col = 'FullRunName',
                                     batch_col = NULL, order_col = NULL, facet_col = NULL)
  
  expect_equal(ncol(df_test), ncol(example_sample_annotation) + ncol(example_proteome) -1)
  expect_equal(nrow(df_test), nrow(example_proteome))
  
  options(warn = 0)
  expect_warning(check_sample_consistency(sample_annotation = NULL, df_long = example_proteome, 
                                          sample_id_col = 'FullRunName',
                                                    batch_col = NULL, order_col = NULL, facet_col = NULL))
  
  falsified_annotation = example_sample_annotation
  colnames(falsified_annotation)[colnames(falsified_annotation) == 'FullRunName'] = 'FalseRunName'
  expect_error(check_sample_consistency(sample_annotation = falsified_annotation, 
                                        df_long = example_proteome, 
                                        sample_id_col = 'FullRunName',
                                        batch_col = NULL, order_col = NULL, facet_col = NULL))
})

test_that("define_sample_order", {
  #TODO: check if the returned class is integer expect_is
  
  order_col <- 'order'
  sample_order = define_sample_order(order_col = order_col, 
                                     sample_annotation = example_sample_annotation, 
                                     facet_col = NULL, batch_col = 'MS_batch', 
                                     df_long = example_proteome, 
                                     sample_id_col = 'FullRunName', 
                                     color_by_batch = TRUE)
  new_order_col = sample_order$order_col
  df_long = sample_order$df_long
  
  expect_is(sample_order, 'list')
  expect_equal(df_long$order_col, example_sample_annotation$order_col)
  
  expect_is(df_long[[new_order_col]], 'numeric')
  
  order_col = NULL
  sample_order = define_sample_order(order_col = order_col, 
                                     sample_annotation = example_sample_annotation, 
                                     facet_col = NULL, batch_col = 'MS_batch', 
                                     df_long = example_proteome, 
                                     sample_id_col = 'FullRunName',
                                     color_by_batch = TRUE)
  new_order_col = sample_order$order_col
  df_long = sample_order$df_long
  
  expect_is(sample_order, 'list')
  expect_equal(df_long$order_col, example_sample_annotation$order_col)
  
  expect_is(df_long[[new_order_col]], 'factor')
})