crested.pl.locus.locus_scoring

crested.pl.locus.locus_scoring(scores, coordinates=None, gene_start=None, gene_end=None, bigwig_values=None, bigwig_midpoints=None, highlight_positions=None, locus_plot_kws=None, bigwig_plot_kws=None, highlight_kws=None, ax=None, **kwargs)

Plot model predictions over a genomic locus from score_gene_locus() and optionally indicate the gene body.

Also plots values from a bigWig file if provided.

Parameters:

• scores (ndarray) – An array of prediction scores for each window.

• coordinates (str | tuple (default: None)) – A string or tuple of coordinates that are being plotted between, to set the x coordinates. Can be a parsable chr:start-region(:strand) string, or a tuple with ((chr), start, end, (strand)), with chr and strand being optional. Will ignore the chromosome and strand, if provided.

• gene_start (int | None (default: None)) – The start position of the gene locus to highlight on the plot.

• gene_end (int | None (default: None)) – The end position of the gene locus to highlight on the plot.

• ylim – Manually set the y-range of the plot.

• bigwig_values (ndarray | None (default: None)) – A numpy array of values extracted from a bigWig file for the same coordinates.

• bigwig_midpoints (list[int] | None (default: None)) – A list of base pair positions corresponding to the bigwig_values.

• highlight_positions (list[tuple[int, int]] | None (default: None)) – A list of tuples specifying ranges to highlight on the plot.

• locus_plot_kws (dict | None (default: None)) – Extra keyword arguments passed to plot() for the prediction plot. Defaults: {'markersize': 5.0, 'linewidth': 2.0, 'color': 'b', 'marker': 'o', 'label': 'Prediction score', 'rasterized': True}.

• bigwig_plot_kws (dict | None (default: None)) – Extra keyword arguments passed to plot() for the bigWig plot. Defaults: {'color': 'b', 'linestyle'='-', 'label': 'bigWig values', 'rasterized': True}.

• highlight_kws (dict | None (default: None)) – Keywords to use for plotting highlights with axvspan(). Default is {‘color’: “green”, ‘alpha’: 0.3}

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

• 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 3 without or 6 with a bigWig plot.

• sharex – Whether to share the x axes of the created plots. Default is True.

• sharey – Whether to share the y axes of the created plots. Default is True.

• kwargs – Additional arguments passed to render_plot() to control the final plot output. Please see render_plot() for details. Custom defaults for locus_scoring: grid='both', xlabel='Genomic position', title='Predictions across genomic regions'(, "bigWig coverage across genomic regions"), ylabel='Prediction_score'(, 'bigWig values').

Return type:

tuple[Figure, Axes] | tuple[Figure, list[Axes]] | None

See also

crested.tl.score_gene_locus, crested.utils.read_bigwig_region

Example

>>> crested.pl.locus.locus_scoring(
...     scores,
...     coordinates=(min_loc, max_loc),
...     gene_start=start,
...     gene_end=end,
...     bigwig_values=bw_values,
...     bigwig_midpoints=midpoints,
...     highlight_positions = [(max_loc-45000, max_loc-40000)],
...     suptitle="CREsted prediction around Elavl2 gene locus for Sst"
... )