alphagenome.visualization.plot.sashimi_plot

Contents

alphagenome.visualization.plot.sashimi_plot#

alphagenome.visualization.plot.sashimi_plot(junctions, ax, interval=None, filter_threshold=0.01, annotate_counts=True, rng=None)[source]#

Plot splice junctions as a Sashimi plot.

Sashimi plots (first described [here](https://arxiv.org/abs/1306.3466) visualize splice junctions from an RNA-seq experiment.

According to the authors, * genomic reads are converted into read densities * junction reads are plotted as arcs whose width is determined by the number of reads aligned to the junction spanning the exons connected by the arc.

Parameters:

  • junctions (Sequence[Junction]) – Splice junctions to plot.

  • ax (Axes) – Matplotlib axis to add the plot to.

  • interval (Optional[Interval] (default: None)) – Interval to plot, used to filter text annotations.

  • filter_threshold (float (default: 0.01)) – Junctions with number of reads below this threshold will be filtered out.

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

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

Contents