Visualization

Visualization and plotting tools.

Plot

visualization.plot.seqlogo(letter_heights[, ...])	Sequence logo plot.
visualization.plot.plot_contact_map(contact_map)	Visualize a contact map.
visualization.plot.plot_track(arr, ax[, x, ...])	Plot a single track on the axis after inferring track type from array.
visualization.plot.plot_tracks(tracks[, x, ...])	Plot multiple tracks as subplots within one matplotlib figure.
visualization.plot.sashimi_plot(junctions, ax)	Plot splice junctions as a Sashimi plot.
visualization.plot.pad_track(track, new_len)	Pad a track with value to the desired length.

Plot components

visualization.plot_components.plot(...[, ...])	Plots AlphaGenome model outputs as individual panels of 'components'.
visualization.plot_components.AbstractComponent()	Abstract base class for plot components.
visualization.plot_components.Tracks(tdata)	Component for visualizing tracks.
visualization.plot_components.OverlaidTracks(tdata)	Component for visualizing overlaid track pairs, such as REF/ALT tracks.
visualization.plot_components.ContactMaps(tdata)	Component for visualizing contact maps.
visualization.plot_components.ContactMapsDiff(tdata)	Component for visualizing contact map differences.
visualization.plot_components.TranscriptAnnotation(...)	Visualizes transcript annotations.
visualization.plot_components.SeqLogo(...[, ...])	Visualizes a sequence logo.
visualization.plot_components.Sashimi(...[, ...])	Visualizes splice junctions as a Sashimi plot.
visualization.plot_components.EmptyComponent([...])	An empty plotting component.
visualization.plot_components.AbstractAnnotation(...)	Abstract base class for plot annotations.
visualization.plot_components.IntervalAnnotation(...)	Visualizes intervals as rectangles across all plot components.
visualization.plot_components.VariantAnnotation(...)	Visualizes variants as thin line-like rectangles across plot components.

Plot transcripts

visualization.plot_transcripts.TranscriptStyle(...)	Style specification for a transcript plot.
visualization.plot_transcripts.TranscriptStylePreset(value)	Style enum for transcript plots.
visualization.plot_transcripts.plot_transcripts(ax, ...)	Plot transcripts.
visualization.plot_transcripts.draw_interval(ax, ...)	Draw rectangle patch on the axis given a genomic interval.
visualization.plot_transcripts.draw_transcript(ax, ...)	Draw an individual transcript as rectangular components on an axis.