alphagenome.visualization.plot.seqlogo

alphagenome.visualization.plot.seqlogo(letter_heights, alphabet='ACGT', one_based=True, start=0, ax=None, letter_colors='default')

Sequence logo plot.

Parameters:

• letter_heights (ndarray) – 2D array with shape (sequence length, len(alphabet)) shape. Positive values indicate that a logo element extends above the horizontal axis, and negative values indicate that the element extends below.

• alphabet (str (default: 'ACGT')) – Alphabet corresponding to the channel axis of letter_heights.

• one_based (bool (default: True)) – If True, plot letters at 1-based coordinates: first letter will be centered at 1. If False, the first letter will be between 0 and 1.

• start (int (default: 0)) – Interval start.

• ax (Optional[Axis] (default: None)) – matplotlib axis to add figures to.

• letter_colors (str (default: 'default')) – Name of the color scheme to use for coloring each letter. Must be one of ‘default’, a scheme consistent with weblogo (gecrooks/weblogo) or ‘factorbook’, a scheme consistent with Factorbook (https://www.factorbook.org/).