crested.pl.locus.track

crested.pl.locus.track(scores, class_idxs=None, zoom_n_bases=None, coordinates=None, class_names=None, highlight_positions=None, plot_kws=None, highlight_kws=None, ax=None, range='deprecated', **kwargs)

Plot a predicted locus track, like a Borzoi prediction or BigWig track.

Parameters:

• scores (ndarray) – A numpy array of heights along the track. Can be shapes (length) or (length, classes), and will automatically squeeze out one-wide dimensions.

• class_idxs (int | list[int] | None (default: None)) – Index or list of indices denoting classes to plot. If None, plots all classes.

• zoom_n_bases (int | None (default: None)) – Number of center bases/bins to zoom in on. Default is None (no zooming).

• coordinates (str | tuple | None (default: None)) – Optional, 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. If strand is provided and ‘-’, runs the x coordinates from end to start.

• class_names (Sequence[str] | str | None (default: None)) – Optional, list of all possible class names to extract label names from. If class_idxs is supplied, picks from there. If not, will use these in order.

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

• plot_kws (dict | None (default: None)) – Extra keyword arguments passed to fill_between().

• highlight_kws (dict | None (default: None)) – Keywords to use for plotting highlights with axvspan(). Default is {‘color’: “green”, ‘alpha’: 0.1}

• 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 20.

• height – Height of the newly created figure if ax=None. Default is 3 per class.

• sharex – Whether to share the y axes of the created plots. Default is False

• 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 track: xlabel=f"{chr}:{start:,.0f}-{end:,.0f} ({end - start} bp)", (if coordinates is set), title=class_names[class_idxs] (if class_names is set)

Return type:

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

See also

crested.pl.render_plot, crested.utils.read_bigwig_region

Example

>>> chrom, start, end = 'chr18', 61010523, 61207131
>>> class_idxs = [output_names_borzoi.index(class_name) for class_name in ['ATAC:MGL', 'ATAC:SSTGA1', 'ATAC:VEC']]
>>> crested.pl.locus.track(
...     borzoi_pred,
...     class_idxs=class_idxs,
...     class_names=output_names_borzoi,
...     coordinates=(chrom, start, end),
...     suptitle="Mouse Borzoi predictions around the FIRE enhancer",
... )

>>> bw_values, midpoints = crested.utils.read_bigwig_region(bw_path, (chrom, start, end))
>>> crested.pl.locus.track(
...     bw_values,
...     coordinates=(chrom, start, end),
...     title="Mouse Borzoi microglia values around the FIRE enhancer",
... )