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)