Sashimi

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Sashimi#

class alphagenome.visualization.plot_components.Sashimi(junction_track, fig_height=1.0, filter_threshold=None, ylabel_template='{name}', ylabel_horizontal=True, annotate_counts=True, normalize_values=True, interval_contained=True, rng=None, color=None)[source]#

Visualizes splice junctions as a Sashimi plot.

Initializes the Sashimi component.

Parameters:

  • junction_track (JunctionData) – A JunctionData object to visualize.

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

  • filter_threshold (float | None (default: None)) – The minimum value for a junction to be included in the plot. This is typically based on the normalized read count. If None, filter out junction values below 5% of the maximum value.

  • ylabel_template (str (default: '{name}')) – A template for the y-axis labels.

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

  • annotate_counts (bool (default: True)) – Whether to annotate the junctions with read counts.

  • normalize_values (bool (default: True)) – Whether to normalize the values to a constant sum.

  • interval_contained (bool (default: True)) – Whether to only plot junctions contained in the interval.

  • rng (Generator | None (default: None)) – Optional random number generator to use for jittering junction paths. If unset will use NumPy’s default random number generator.

  • color (str | None (default: None)) – Color of the Sashimi arcs.

Methods

get_ax_height(axis_index)

Returns the height of the axis.

plot_ax(ax, axis_index, interval)

Plots the Sashimi plot on the given axis.
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