tests/testthat/test-0_plot_sample_clustering_b.R

In familiar: End-to-End Automated Machine Learning and Model Evaluation

# Don't perform any further tests on CRAN due to time of running the complete
# test.
testthat::skip_on_cran()
testthat::skip_on_ci()

debug_flag <- FALSE

# Generic test
familiar:::test_plots(
  plot_function = familiar:::plot_sample_clustering,
  not_available_all_predictions_fail = FALSE,
  not_available_some_predictions_fail = FALSE,
  outcome_type_available = c("count", "continuous", "binomial", "multinomial", "survival"),
  data_element = "feature_expressions",
  plot_args = list(
    "verbose" = FALSE,
    "show_normalised_data" = "set_normalisation"),
  debug = debug_flag
)

# No extra elements
familiar:::test_plot_ordering(
  plot_function = familiar:::plot_sample_clustering,
  data_element = "feature_expressions",
  outcome_type_available = c("count", "continuous", "binomial", "multinomial", "survival"),
  plot_args = list(
    "facet_by" = c("learner", "fs_method", "data_set"),
    "x_axis_by" = "sample",
    "y_axis_by" = "feature",
    "show_outcome" = FALSE,
    "show_feature_dendrogram" = FALSE,
    "show_sample_dendrogram" = FALSE,
    "verbose" = FALSE),
  debug = debug_flag
)

# No normalisation.
familiar:::test_plot_ordering(
  plot_function = familiar:::plot_sample_clustering,
  data_element = "feature_expressions",
  outcome_type_available = c("count", "continuous", "binomial", "multinomial", "survival"),
  plot_args = list(
    "facet_by" = c("learner", "fs_method", "data_set"),
    "show_normalised_data" = "none",
    "verbose" = FALSE),
  debug = debug_flag
)

# Normalisation per dataset.
familiar:::test_plot_ordering(
  plot_function = familiar:::plot_sample_clustering,
  data_element = "feature_expressions",
  outcome_type_available = c("count", "continuous", "binomial", "multinomial", "survival"),
  plot_args = list(
    "facet_by" = c("learner", "fs_method", "data_set"),
    "show_normalised_data" = "set_normalisation",
    "verbose" = FALSE),
  debug = debug_flag
)


# With sample limit
familiar:::test_plot_ordering(
  plot_function = familiar:::plot_sample_clustering,
  data_element = "feature_expressions",
  outcome_type_available = c("count", "continuous", "binomial", "multinomial", "survival"),
  plot_args = list(
    "facet_by" = c("learner", "fs_method", "data_set"),
    "sample_limit" = 20L,
    "verbose" = FALSE),
  debug = debug_flag
)


# Test multiple evaluation times
familiar:::test_plot_ordering(
  plot_function = familiar:::plot_sample_clustering,
  data_element = "feature_expressions",
  outcome_type_available = c("survival"),
  plot_args = list(
    "evaluation_times" = c(500, 1000, 1500, 2000),
    "verbose" = FALSE),
  debug = debug_flag
)