Viewer

class pygv.viewer.GenomeViewer(font_name=None, font_size=None, alternative_color_map=None, hspace=0.2, inward_ticks=None, n_ticks=None)

Genome Viewer

Examples

>>> from pygv.viewer import GenomeViewer
>>> from pygv.tracks import gtf_track
>>> gv = GenomeViewer()
>>> gencode_track = gtf_track.GtfTrack(
>>>     "~/gencode.v34lift37.annotation.sorted.gtf.gz",
>>>     name="GENCODE", show_genes=True, show_transcript_id=True,
>>>     filters=lambda x: x.transcript_id in {"ENST00000332995.11_1", "ENSG00000112137.17_4",
>>>                                           "ENST00000379350.5_1", "ENST00000379335.7_1"},
>>>     annotation_formatter=lambda x: x.split(".")[0]
>>> )
>>> gv.add_track(gencode_track)
>>> gv.plot("chr6", 12714999, 13292716)
>>> plt.show()

add_group_autoscale(track_idx: tuple[int, ...] | list[int])

Add group autoscale

Parameters:

track_idx (Union[tuple[int, ...], list[int]]) – Indexes of the tracks to be scaled together

Examples

(Source code)

(png, pdf)

(png, pdf)

(png, pdf)

add_group_autoscale_by_name(track_name: tuple[str, ...] | list[str])

Add group autoscale

Parameters:

track_name (Union[tuple[str, ...], list[str]]) – Names of the tracks to be scaled together

add_group_label(start_track_idx: int, end_track_idx: int, label: str, x=0.02, x_line_offset=0.015)

Add group label

Parameters:

• start_track_idx (int) – Index of the start track (0-based)

• end_track_idx (int) – Index of the end track (0-based)

• label (str) – Group label

• x (float) – X-position for the label in figure coordinates (default 0.02).

• x_line_offset (float) – Offset for the line from the label in figure coordinates (default 0.015).

Examples

(Source code)

(png, pdf)

(png, pdf)

(png, pdf)

add_group_label_by_name(start_track_name: str, end_track_name: str, label: str, x=0.02, x_line_offset=0.015)

Add group label by track names

Parameters:

• start_track_name (str) – Name of the start track

• end_track_name (str) – Name of the end track

• label (str) – Group label

• x (float) – X-position for the label in figure coordinates (default 0.02).

• x_line_offset (float) – Offset for the line from the label in figure coordinates (default 0.015).

add_track(track: Track) → None

Add a track to a GenomeViewer instance

Parameters:

track (tracks.track.Track) – Track object to be added

add_tracks(tracks)

Add tracks to a GenomeViewer instance

Parameters:

tracks (tuple or list) – Objects of tracks.track.Track to be added

plot(chromosome, start, end, fig_width=8, height_scale_factor=1, force_tight_layout=None, fig_height=None, **kwargs)

Plot the genome viewer with the registered tracks.

Parameters:

• chromosome (str) – Chromosome/contig the region locates.

• start (int) – Start of the genomic region, 0-based.

• end (int) – End of the genomic region, 0-based.

• fig_width (float, optional) – Width (in inches) of the figure. Default is 8.

• height_scale_factor (float, optional) – Aspect ratio of the figure, so that height_scale_factor * fig_width gives the height of the figure. Default is 1.

• force_tight_layout (bool or None, optional) – If True, PyGV applies tight layout to the figure. Default is None.

• fig_height (float or None, optional) – Height of the figure. If None, height will be the sum of tracks’ heights (in unit) * height_scale_factor. Default is None.

• **kwargs (dict, optional) – Additional keyword arguments for track customization.

Returns:

Axes for each track.

Return type:

list of matplotlib.pyplot.Axes

remove_track(track)

Remove a track from a GenomeViewer instance

Parameters:

track (tracks.track.Track) – Track object to be removed

reset_group_autoscale()

Remove all group autoscale rules

save(*args, **kwargs)

Save figure to a file

Parameters:

• args

• kwargs

set_global_highlight_region(start: int, end: int, color='yellow', alpha=0.3)

Set a global highlight region across all tracks, including the spaces between subplots.

Parameters:

• start (int) – Start position of the highlight region (genomic coordinate).

• end (int) – End position of the highlight region (genomic coordinate).

• color (str, optional) – Color of the highlight region. Default is “yellow”.

• alpha (float, optional) – Transparency level of the highlight region. Default is 0.3.

Return type:

None

set_highlight_regions(starts: list | tuple, ends: list | tuple, colors=(), alpha_vals=())

Set highlight regions for all tracks. If you only want to highlight regions on specific tracks, you can call each track’s set_highlight_regions() method. Chromosome name is not needed for this method, it will use the same chromosome name when you call the plot() method.

Parameters:

• starts (Union[list, tuple]) – Start positions

• ends (Union[list, tuple]) – End positions

• colors (tuple) – Leave it as an empty tuple if you want to use the default color. If you only give one color, it will be applied to all regions; otherwise, you should specify colors for each region.

• alpha_vals (tuple) – Leave it as an empty tuple if you want to use the default transparency level (0.5). If you only give one value, it will be applied to all regions; otherwise, you should specify transparency values for each region.

Examples

(Source code, png, pdf)

show_tracks()

Show all registered tracks

Returns:

tracks – A list of registered tracks. Each element is also a list: name of the track, track type, track.

Return type:

list