def test_cli_pipeline_with_figures(): args = [ "deva", "tests/pidgin_values.csv", "tests/pidgin_annotations.csv", "--iqrs", "1.5", "--up_or_down", "up", "--output_prefix", "tests/output/pipeline_figs_test", "--ind_sep", "-", "--frac_filter", "0.10", "--write_comparison_summaries", "--fdr", "0.5", "--write_gene_list", "--make_heatmaps", "--red_or_blue", "blue", ] _main(args)
def test_cli_normer(): args = [ "normalize", "tests/pidgin_values.csv", "--output_prefix", "tests/output/normer", ] _main(args)
def test_cli_outliers_table(): args = [ "outliers_table", "tests/pidgin_values.csv", "--iqrs", "1.5", "--up_or_down", "up", "--output_prefix", "tests/output/outliers_table_test", "--ind_sep", "-", "--write_frac_table", ] _main(args)
def test_vis(): args = [ "visualize", "tests/pidgin_qvalues.csv", "tests/pidgin_annotations.csv", "tests/pidgin_fracTable.csv", "fisherFDR_comp0_1", "--annotations_to_show", "comp0 comp1", "--output_prefix", "tests/output/vis_cli_test", "--write_gene_list", "--fdr", "0.5", "--red_or_blue", "red", ] _main(args)
def test_cli_pipeline(): args = [ "deva", "tests/pidgin_values.csv", "tests/pidgin_annotations.csv", "--iqrs", "1.5", "--up_or_down", "up", "--output_prefix", "tests/output/pipeline_test", "--write_frac_table", "--write_outlier_table", "--ind_sep", "-", "--frac_filter", "0.10", "--write_comparison_summaries", ] _main(args)
def test_cli_compare_groups_with_heatmaps(): args = [ "compare_groups", "tests/pidgin_outliers.csv", "tests/pidgin_annotations.csv", "--iqrs", "1.5", "--up_or_down", "up", "--output_prefix", "tests/output/compare_groups_test", "--frac_filter", "0.1", "--write_comparison_summaries", "--make_heatmaps", "--write_gene_list", "--fdr", "0.6", "--red_or_blue", "red", ] _main(args)