Tracks for genome annotations#

BED-like#

If you want to plot interactions and paired-end data, consider use BedPETrack or ConnectionArcTrack in PyGV.

class pygv.tracks.bed_track.BedTrack(track, **kwargs: Any)#

If you’re looking to visualize genomic features like genes and regulatory elements, you can utilize the BedTrack in PyGV. If you desire greater control over the specific features to be plotted, such as filtering features by names, gene IDs, or transcript IDs, then the GtfTrack may be the preferred choice.

Parameters:

  • track (str) –

    Path to the input bed file. Index from tabix is optional, but when index presents, drawing will be much faster and less memory intensive. PyGV’s BedTrack implementation supports the visualization of genomic features encoded in four BED variations:

    • Bed3: includes three columns: chromosome, start, and end.

    • Bed4: includes three columns: chromosome, start, end, and name.

    • Bed8: extends Bed3 with additional columns for name, score, strand, thickStart, and thickEnd.

    • Bed12: the most comprehensive, includes columns for itemRgb, blockCount, blockSizes, and blockStarts in addition to those found in Bed8.

  • kwargs (Any) –

    heightfloat

    Height of each feature lane. If you have four feature lanes, and the height value is set as 0.25, then the final track will have identical overall height as other tracks. If you have multiple BedTrack or other kind of AnnotationTrack, you can set the same height values to all these tracks, which makes sure all tracks have consistent appearances (which is also the default behavior).

    allowed_feature_lanesOptional[int]

    See allowed_feature_lanes

    plot_thicknessbool

    See plot_thickness

    padding_leftint or float

    See padding_left

    namestr

    Track name. name

    show_namebool

    Show feature names. See show_name

    More kwargs can be seen here: AnnotationTrack

Examples

(Source code, png, pdf)

_images/plot_bed.png
property plot_thickness#

When valid starting (thickStart) and ending (thickEnd) positions are provided for a feature, as observed, for instance, in the region between the start and stop codon within gene displays, this specific region will be illustrated with a thicker line. In situations where there is no valid thick section, whether due to the absence of thickStart and thickEnd positions (as in the case of providing a bed3 file) or when the length of the feature is less than 1, the plot_thickness property will be automatically set to False.

property show_mode#

Collapse overlapping features (collapsed) or keep them separately (expanded) for plotting.

property block_line_width#

Line/edge width for blocks.

class pygv.tracks.bed_track.BedPETrack(track, **kwargs: Any)#

If you’re looking to visualize genomic interactions like proximity captured by Hi-C, you can utilize the BedPETrack in PyGV.

Parameters:

  • track (str) – Path to the input BEDPE file. Index from tabix is optional, but when index presents, drawing will be much faster and less memory intensive. Only the first six columns in the file will be used (chromosome, start, and end for the two anchors)

  • kwargs (dict) –

    namestr

    Track name. name

    show_namebool

    Show feature names. See show_name

    flipbool

    Flip the arcs vertically

    highlight_linkslist or tuple

    Links to highlight. Each item can be either a BEDPE name string or a coordinate tuple/list of (chromosome, start1, end1, start2, end2).

    highlight_link_colorcolor_like

    Color used for highlighted links.

    highlight_link_alphafloat

    Alpha used for highlighted links.

    highlight_link_line_widthfloat

    Line width used for highlighted links.

    More kwargs can be seen here: AnnotationTrack

Examples

(Source code, png, pdf)

_images/plot_bedpe.png

Set highlighted links for this BEDPE track.

Parameters:

links (str or iterable) – A BEDPE name, or an iterable of names and/or coordinate tuples (chromosome, start1, end1, start2, end2).

Add one highlighted link by BEDPE name or anchor coordinates.

Remove all highlighted links.

class pygv.tracks.bed_track.ConnectionArcTrack(track, **kwargs)#

Similar to BedPETrack, ConnectionArcTrack can be used to visualize genomic interactions like enhancer-promoter interaction. The main difference between these two tracks is that ConnectionArcTrack draws a directed arrow from the source to the target.

Parameters:

  • track (str) – Path to the input BEDPE file. Index from tabix is optional, but when index presents, drawing will be much faster and less memory intensive. Only the first six columns in the file will be used (chromosome, start, and end for the two anchors)

  • kwargs (dict) –

    namestr

    Track name. name

    show_namebool

    Show feature names. See show_name

    flipbool

    Flip the arcs vertically

    More kwargs can be seen here: AnnotationTrack

Examples

(Source code, png, pdf)

_images/plot_bedpe.png

bigBed#

class pygv.tracks.bigbed_track.BigBed6Track(track, **kwargs)#

Standard BigBed6 track

Parameters:

Examples

(Source code, png, pdf)

_images/plot_bigbed.png
get_filters()#

Return filters

set_filters(key, value)#

Set filter, records with matching names will be labeled

Parameters:

  • key (str) – Currently, only name is supported

  • value (str)

class pygv.tracks.bigbed_track.UCSCMutationTrack(track, **kwargs)#

Lollipop plot from UCSC-style mutational bigwig files

Parameters:
property apply_color_gradient#

Set it to True to apply color gradient to marks, by default, False

property color_map#

Color map for markers

get_filters()#

Return filters

property line_color#

Line color, by default, red

set_filters(key, value)#

Set filter, records matching filters will be labeled in the track

Parameters:

  • key (str) – Only “MAF” and “ID” are supported currently

  • value (numeric) – min value

GTF/GFF#

class pygv.tracks.gtf_track.GtfTrack(track, filters=None, show_genes=False, annotation_formatter=None, **kwargs)#

Gtf track

Parameters:
property filters#

Filters, a callable object which returns True/False to keep/discard gtf records. Set as None to disable this function.

property show_transcript_id#

Filters, a callable object which returns True/False to keep/discard gtf records. Set as None to disable this function.