Tracks for alignments#
BAM#
- class pygv.tracks.bam_track.CollapsedReadTrack(track, **kwargs)#
Plot collapsed reads (only 5’ end and the span)
- Parameters:
track
kwargs –
- patch_height :
- line_color :
- max_num_read :
- pileup_offset :
Examples
(
Source code,png,pdf)
- property line_color#
Line color, by default, #96B8C8
- property max_num_read#
Max number of reads in the visible window, if there are more reads, random downsampling will be used
- property patch_height#
Height of patches (for exons/blocks)
- property pileup_offset#
offset of pileup, by default, 0.1
- class pygv.tracks.bam_track.CoverageTrack(track, filters=None, **kwargs)#
Bam coverage track
Examples
(
Source code,png,pdf)
- class pygv.tracks.bam_track.ReadArcTrack(track, filters=None, **kwargs)#
Plot read in arcs
Examples
(
Source code,png,pdf)
- class pygv.tracks.bam_track.SplicedReadTrack(track, **kwargs)#
Plot spliced reads
- Parameters:
track
kwargs –
- padding_left :
- padding_right :
- show_name :
- patch_height :
- lane_space :
- features_per_lane :
- line_color :
Examples
(
Source code,png,pdf)
- property features_per_lane#
Features per lane
- property lane_space#
Extra spaces between lanes
- property line_color#
Line color
- property padding_left#
Units adding to the left of features (adding places for text labels)
- property padding_right#
Units adding to the right of features (adding places for text labels)
- property patch_height#
Height of patches (for exons/blocks)
- property show_name#
Units adding to the right of features (adding places for text labels)
- class pygv.tracks.bam_track.StrandSpecificCoverageTrack(track, filters=None, **kwargs)#
Draw strand-specific coverages from bam file
Examples
(
Source code,png,pdf)
