tacco.plots.significances

significances(significances, p_key, value_key, group_key, enrichment_key='enrichment', enriched_label='enriched', pmax=0.05, pmin=1e-05, annotate_pvalues=True, value_cluster=False, group_cluster=False, value_order=None, group_order=None, axsize=None, ax=None, scale_legend=1.0)[source]

Plot enrichment significances.

Parameters:

  • significances – A DataFrame with p-values and their annotation. If it contains significances for enrichment and depletion, this direction has to be specified with values “enriched” and something else (e.g. “depleted” or “purified”) in a column “enrichment” of the DataFrame. See also the parameters enrichment_key and enrichment_label.

  • p_key – The key with the p-values.

  • value_key – The key with the values for which the enrichment was determined.

  • group_key – The key with the groups in which the enrichment was determined.

  • enrichment_key – The key with the direction of enrichment, i.e something like “enriched” and “purified”. See also parameter enriched_label. Default: “enrichment”.

  • enriched_label – The value under the key enrichment_key which indicates something like enrichment. Default: “enriched”.

  • pmax – The maximum p-value to show.

  • pmin – The minimum p-value on the color scale.

  • annotate_pvalues – Whether to annotate p-values

  • value_cluster – Whether to cluster and reorder the values.

  • group_cluster – Whether to cluster and reorder the groups.

  • value_order – Set the order of the values explicitly with a list or to be close to diagonal by specifying “diag”; this option is incompatible with value_cluster.

  • group_order – Set the order of the groups explicitly with a list or to be close to diagonal by specifying “diag”; this option is incompatible with group_cluster.

  • axsize – Tuple of width and size of a single axis. If None, use automatic values.

  • ax – The Axes to plot on. If None, creates a fresh figure for plotting. Incompatible with dendrogram plotting.

  • scale_legend – Set to scale height and width of legend.

Returns:

A Figure.