SeqLogo

class alphagenome.visualization.plot_components.SeqLogo(scores, scores_interval, fig_height=1.0, alphabet='ACGT', max_width=1000, ylabel='', ylabel_horizontal=True, ylim=None, **kwargs)

Visualizes a sequence logo.

Initializes the SeqLogo component.

Parameters:

• scores (Float32[ndarray, 'S A']) – A numpy array of shape (sequence_length, alphabet_size) containing the sequence logo scores.

• scores_interval (Interval) – The genomic interval corresponding to the scores.

• fig_height (float (default: 1.0)) – The height of the figure.

• alphabet (str (default: 'ACGT')) – The alphabet used in the sequence logo.

• max_width (int (default: 1000)) – The maximum width of the sequence logo to plot.

• ylabel (str (default: '')) – An optional label for the y-axis.

• ylabel_horizontal (bool (default: True)) – Whether to make the y-axis label horizontal.

• ylim (tuple[float, float] | None (default: None)) – An optional range to set for the y-axis.

• **kwargs – Additional keyword arguments to pass to the plotting function.

Methods

get_ax_height(axis_index)	Returns the height of the axis.
plot_ax(ax, axis_index, interval)	Plots the sequence logo on the given axis.