/BioGraPy

Biological Graphic tool in Python

Primary LanguagePythonOtherNOASSERTION

BioGraPy - Biological Graphical Library in Python

Fork that adds support to plot the tracks below an existing figure, and adds some new features to draw such as text sequence with automatic font size and highlighted text.

import matplotlib
import matplotlib.pyplot as plt
from matplotlib.font_manager import FontProperties
import numpy as np

import biograpy
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio.Seq import Seq


fig1, ax = plt.subplots(figsize=(10,3), dpi=300)

ax.scatter(x=list(range(0, 1200)), y=np.random.random(1200))
ax.set_xlim([0,1200])
ax.set_ylim([0,2])

# We use the package biograpy to create Panel, tracks, and features
panel = biograpy.Panel(fig1)
track = biograpy.tracks.BaseTrack()

# Simple feature drawn as a rectangle
track.add_feature(biograpy.features.Simple(name='Simple1', start = 50, end = 300))

# Gene feature drawn as an arrow
genefeat = SeqFeature(FeatureLocation(100,500), type='gene', strand=1)
track.add_feature(biograpy.features.GeneSeqFeature(genefeat, name='GeneSeqFeature1'))

# Simple feature with color
track.add_feature(biograpy.features.Simple(name='Simple_colored1', start = 500, end = 820, color_by_cm=False, fc='r'))

# Gene feature with color
track.add_feature(biograpy.features.GeneSeqFeature(genefeat,name='GeneSeqFeature2_colored',fc='r'))

# Very short gene feature (to test the arrow head automatic sizing)
genefeat = SeqFeature(FeatureLocation(800,810), type='gene', strand=1)
track.add_feature(biograpy.features.GeneSeqFeature(genefeat, name='GeneSeqFeature_very_short'))

# mRNA with one CDS drawn as a shaded rectangle with an arrow on top
CDS_feature = SeqFeature(FeatureLocation(180,1000), type='CDS', strand=-1)
mRNA_feature = SeqFeature(FeatureLocation(180,1100), type='mRNA', strand=-1)
mRNAandCDSfeat = biograpy.features.CoupledmRNAandCDS(mRNA_feature, CDS_feature,
                                                     name='CoupledmRNAandCDS1_strandm', ec='k')
track.add_feature(mRNAandCDSfeat)

# mRNA with CDS, custom color
CDS_feature = SeqFeature( FeatureLocation(200,600), type='CDS', strand=1)
mRNA_feature = SeqFeature( FeatureLocation(100,800), type='mRNA', strand=1)
mRNAandCDSfeat = biograpy.features.CoupledmRNAandCDS(mRNA_feature, CDS_feature,
                                                     name='CoupledmRNAandCDS1_strandp_colored', ec='r', fc='r')
track.add_feature(mRNAandCDSfeat)

# Very short mRNA with CDS (to test the arrow head automatic sizing)
CDS_feature = SeqFeature( FeatureLocation(250,260), type='CDS', strand=1)
mRNA_feature = SeqFeature( FeatureLocation(220,300), type='mRNA', strand=1)
mRNAandCDSfeat = biograpy.features.CoupledmRNAandCDS(mRNA_feature, CDS_feature,
                                                     name='CoupledmRNAandCDS1_very_short')
track.add_feature(mRNAandCDSfeat)

# Gene feature on minus strand
geneSeqfeat = SeqFeature( FeatureLocation(900,200), type = 'gene', strand=-1)
genefeat = biograpy.features.GeneSeqFeature(geneSeqfeat, name='GeneSeqFeature3_strandm')
track.add_feature(genefeat)

track2 = biograpy.tracks.BaseTrack(biograpy.features.Simple(name='Simple3_track2', start= 0, end = 80))

panel.add_track(track)
panel.add_track(track2)
panel._draw_tracks()
panel.save('biograpy_test1.png')

example1

fig1, ax = plt.subplots(figsize=(11,3), dpi=400)

ax.scatter(x=list(range(0, 100)), y=np.random.random(100))
ax.set_xlim([0,100])
ax.set_ylim([0,2])

# Create panel and track
panel = biograpy.Panel(fig1)
track = biograpy.tracks.BaseTrack()

# Text sequence feature
track.add_feature(biograpy.features.TextSequence(
        'MKKVIVIGVNHAGTSFIRTLLSKSKDFQVNAYDRNTNISFLGCGIALAVSGVVKNTEDLFYSTPEELKAMGANVFMAHDVVGLDLDKKQVIVKDL',
        start=10, name="TextSequence1"))

"""
Pretty text sequence feature allows to pass a text sequence together with a list of regions
to highlight. The font size is calculated automatically to fit the scale of the x axis.
"""

prettyTextFeat = biograpy.features.PrettyTextSequence(
    'KSKDFQVNAYDRNMKKVIVIGVNHAGTSFIRTLLSKSKDFQVNAYDRNTNISFLGCGIALAVSGVVKNTEDLFYSTPEELKAMGANVFMAHDVVGLDLDKKQVIVKDLATGKETVDHY',
    highlightList=[{'start':0, 'end':10, 'background_color':'red', 'background_color_alpha':0.4, 'weight':900},
                   {'start':20, 'end':25, 'foreground_color':'blue', 'weight':100}
                  ],
    start=20, name='PrettyTextSequence1')
track.add_feature(prettyTextFeat)

panel.add_track(track)
panel.save('biograpy_test2.png')
panel._draw_tracks()

example1