crested.pl.hist.locus_scoring

crested.pl.hist.locus_scoring(scores, range, gene_start=None, gene_end=None, title='Predictions across Genomic Regions', ylim=None, bigwig_values=None, bigwig_midpoints=None, filename=None, grid=True, figsize=(30, 5), highlight_positions=None, marker_size=5.0, line_width=2.0)

Plot the predictions as a line chart over the entire genomic input and optionally indicate the gene locus.

Also plots values from a bigWig file if provided.

Parameters:

• scores – An array of prediction scores for each window.

• range – The genomic range of the input.

• model_class – The class index to plot from the prediction scores.

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

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

• title (default: 'Predictions across Genomic Regions') – The title of the plot.

• ylim (default: None) – Manually set the y-range of the plot.

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

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

• filename (default: None) – The filename to save the plot to.

• grid (default: True) – Add grid to plot.

• figsize (default: (30, 5)) – Size of figure.

• highlight_positions (default: None) – A list of tuples specifying ranges to highlight on the plot.

• marker_size (default: 5.0) – Size of the markers in the plot. Default is 5.0.

• line_width (default: 2.0) – Width of the lines in the plot. Default is 2.0.

See also

crested.tl.Crested.score_gene_locus, crested.utils.read_bigwig_region

Example

>>> crested.pl.hist.locus_scoring(
...     scores,
...     range=(0, 1000),
...     gene_start=100,
...     gene_end=200,
...     title="Predictions across Genomic Regions",
...     bigwig_values=bigwig_values,
...     bigwig_midpoints=bigwig_midpoints,
... )