def gene_panel(self, ax, feature):
"""
Plots gene models on an Axes.
Queries the database
:param ax: matplotlib.Axes object
:param feature: pybedtools.Interval
"""
from gffutils.contrib.plotting import Gene
extent = [feature.start, feature.stop]
nearby_genes = self.db.region((feature.chrom, feature.start, feature.stop), featuretype="gene")
ybase = 0
ngenes = 0
for nearby_gene in nearby_genes:
ngenes += 1
extent.extend([nearby_gene.start, nearby_gene.stop])
gene_collection = Gene(
self.db,
nearby_gene,
transcripts=["mRNA"],
cds=["CDS"],
utrs=["exon"],
ybase=ybase,
color="0.5",
picker=5,
)
gene_collection.name = nearby_gene.id
gene_collection.add_to_ax(ax)
ybase += gene_collection.max_y
xmin = min(extent)
xmax = max(extent)
ymax = ngenes
# 1% padding seems to work well
padding = (xmax - xmin) * 0.01
ax.axis("tight")
# add lines indicating extent of current feature
vline_kwargs = dict(color="k", linestyle="--")
ax.axvline(feature.start, **vline_kwargs)
ax.axvline(feature.stop, **vline_kwargs)
# Make a new feature to represent the region plus surrounding genes
interval = pybedtools.create_interval_from_list(feature.fields)
interval.start = xmin - padding
interval.stop = xmax + padding
interval.strand = "."
return interval
def gene_panel(self, ax, feature):
"""
Plots gene models on an Axes.
Queries the database
:param ax: matplotlib.Axes object
:param feature: pybedtools.Interval
"""
from gffutils.contrib.plotting import Gene
extent = [feature.start, feature.stop]
nearby_genes = self.db.overlapping_features(feature.chrom,
feature.start,
feature.stop,
featuretype='gene')
ybase = 0
ngenes = 0
for nearby_gene in nearby_genes:
ngenes += 1
extent.extend([nearby_gene.start, nearby_gene.stop])
gene_collection = Gene(self.db,
nearby_gene,
transcripts=['mRNA'],
cds=['CDS'],
utrs=['exon'],
ybase=ybase,
color="0.5",
picker=5)
gene_collection.name = nearby_gene.id
gene_collection.add_to_ax(ax)
ybase += gene_collection.max_y
xmin = min(extent)
xmax = max(extent)
ymax = ngenes
# 1% padding seems to work well
padding = (xmax - xmin) * 0.01
ax.axis('tight')
# add lines indicating extent of current feature
vline_kwargs = dict(color='k', linestyle='--')
ax.axvline(feature.start, **vline_kwargs)
ax.axvline(feature.stop, **vline_kwargs)
# Make a new feature to represent the region plus surrounding genes
interval = pybedtools.create_interval_from_list(feature.fields)
interval.start = xmin - padding
interval.stop = xmax + padding
interval.strand = '.'
return interval
"""
Example to plot random genes
"""
import gffutils
from gffutils.contrib.plotting import Gene
from pylab import *
G = gffutils.FeatureDB('dmel-all-no-analysis-r5.43.gff.db')
gene = G.random_feature('gene')
gene_collection = Gene(
G,
gene,
utrs=['three_prime_UTR', 'five_prime_UTR'],
color="0.5",
edgecolor="None")
fig = figure()
ax = fig.add_subplot(111)
gene_collection.add_to_ax(ax)
ax.axis('tight')
show()
def genes_panel(self, ax, feature):
"""
Plots gene models on an Axes.
Queries the database
:param ax: matplotlib.Axes object
:param feature: pybedtools.Interval
"""
from gffutils.contrib.plotting import Gene
extent = [feature.start, feature.stop]
nearby_genes = self.db.region((feature.chrom, feature.start, feature.stop), featuretype="gene")
ybase = 0
ngenes = 0
for nearby_gene in nearby_genes:
# TODO: there should be a better way of identifying which gene is
# the same as the feature requested. Might need to expose an "ID"
# kwarg.
try:
if nearby_gene["ID"][0] == feature["ID"]:
color = "0.2"
else:
color = "0.5"
except KeyError:
color = "0.5"
ngenes += 1
extent.extend([nearby_gene.start, nearby_gene.stop])
gene_collection = Gene(
self.db, nearby_gene, transcripts=None, cds=["CDS"], utrs=["exon"], ybase=ybase, color=color
)
gene_collection.name = nearby_gene.id
gene_collection.add_to_ax(ax)
ybase += gene_collection.max_y
xmin = min(extent)
xmax = max(extent)
ymax = ngenes
# 1% padding seems to work well
padding = (xmax - xmin) * 0.01
ax.axis("tight")
# add lines indicating extent of current feature
# vline_kwargs = dict(color='k', linestyle='--')
# ax.axvline(feature.start, **vline_kwargs)
# ax.axvline(feature.stop, **vline_kwargs)
# Make a new feature to represent the region plus surrounding genes
interval = pybedtools.create_interval_from_list(feature.fields)
interval.strand = "."
for txt in ax.get_yticklabels():
txt.set_visible(False)
for tick in ax.get_yticklines():
tick.set_visible(False)
ax.set_ylabel("Genes")
ax.spines["right"].set_color("None")
ax.spines["left"].set_color("None")
ax.spines["top"].set_color("None")
ax.yaxis.set_ticks_position("none")
ax.xaxis.set_ticks_position("bottom")
ax.set_ylabel("Genes", rotation=0, horizontalalignment="right", verticalalignment="center")
return interval
"""
Example to plot random genes
"""
import gffutils
from gffutils.contrib.plotting import Gene
from pylab import *
G = gffutils.FeatureDB('dmel-all-no-analysis-r5.43.gff.db')
gene = G.random_feature('gene')
gene_collection = Gene(G,
gene,
utrs=['three_prime_UTR', 'five_prime_UTR'],
color="0.5",
edgecolor="None")
fig = figure()
ax = fig.add_subplot(111)
gene_collection.add_to_ax(ax)
ax.axis('tight')
show()
def genes_panel(self, ax, feature):
"""
Plots gene models on an Axes.
Queries the database
:param ax: matplotlib.Axes object
:param feature: pybedtools.Interval
"""
from gffutils.contrib.plotting import Gene
extent = [feature.start, feature.stop]
nearby_genes = self.db.region(
(feature.chrom, feature.start, feature.stop), featuretype='gene')
ybase = 0
ngenes = 0
for nearby_gene in nearby_genes:
# TODO: there should be a better way of identifying which gene is
# the same as the feature requested. Might need to expose an "ID"
# kwarg.
try:
if nearby_gene['ID'][0] == feature['ID']:
color = '0.2'
else:
color = '0.5'
except KeyError:
color = '0.5'
ngenes += 1
extent.extend([nearby_gene.start, nearby_gene.stop])
gene_collection = Gene(self.db,
nearby_gene,
transcripts=None,
cds=['CDS'],
utrs=['exon'],
ybase=ybase,
color=color)
gene_collection.name = nearby_gene.id
gene_collection.add_to_ax(ax)
ybase += gene_collection.max_y
xmin = min(extent)
xmax = max(extent)
ymax = ngenes
# 1% padding seems to work well
padding = (xmax - xmin) * 0.01
ax.axis('tight')
# add lines indicating extent of current feature
# vline_kwargs = dict(color='k', linestyle='--')
# ax.axvline(feature.start, **vline_kwargs)
# ax.axvline(feature.stop, **vline_kwargs)
# Make a new feature to represent the region plus surrounding genes
interval = pybedtools.create_interval_from_list(feature.fields)
interval.strand = '.'
for txt in ax.get_yticklabels():
txt.set_visible(False)
for tick in ax.get_yticklines():
tick.set_visible(False)
ax.set_ylabel('Genes')
ax.spines['right'].set_color('None')
ax.spines['left'].set_color('None')
ax.spines['top'].set_color('None')
ax.yaxis.set_ticks_position('none')
ax.xaxis.set_ticks_position('bottom')
ax.set_ylabel('Genes',
rotation=0,
horizontalalignment='right',
verticalalignment='center')
return interval
