crested.pl.modisco.similarity_heatmap

crested.pl.modisco.similarity_heatmap(similarity_matrix, indices, cmap='coolwarm', plot_kws=None, ax=None, fig_size='deprecated', fig_path='deprecated', **kwargs)

Plot a similarity heatmap of all pattern indices.

Parameters:

• similarity_matrix (ndarray) – A 2D numpy array containing the similarity values.

• indices (list) – List of pattern indices.

• cmap (str | Colormap (default: 'coolwarm')) – Colormap to use.

• plot_kws (dict | None (default: None)) – Extra keyword arguments passed to heatmap(). Adjusted defaults compared to the base function are {'annot': True, 'fmt': '.2f', 'annot_kws': {'size': 8}, 'xticklabels': indices, 'yticklabels': indices}.

• ax (Axes | None (default: None)) – Axis to plot values on. If not supplied, creates a figure from scratch.

• width – Width of the newly created figure if ax=None. Default is 30.

• height – Height of the newly created figure if ax=None. Default is 15.

• kwargs – Additional arguments passed to render_plot() to control the final plot output. Please see render_plot() for details. Adjusted defaults for similarity_heatmap: title="Pattern similarity heatmap", title_fontsize=20, [x/y]label='Pattern index', [x/y]label_fontsize=15

Return type:

tuple[Figure, Axes] | None

See also

crested.tl.modisco.calculate_similarity_matrix

Examples

>>> sim_matrix, indices = crested.tl.modisco.calculate_similarity_matrix(
...     all_patterns
... )
>>> crested.pl.modisco.similarity_heatmap(sim_matrix, indices, fig_size=(42, 17))