"""
Module for the BedExtendableHeatmap class, which adds bed track plotting
functionality for the extendable heatmap system.
"""
import matplotlib as mpl
from lib5c.plotters.extendable import BaseExtendableHeatmap
from lib5c.util.bed import check_intersect
[docs]class BedExtendableHeatmap(BaseExtendableHeatmap):
"""
ExtendableHeatmap mixin class providing bed track plotting functionality.
"""
[docs] def add_bed_tracks(self, bed_tracks, size='3%', pad=0.0, axis_limits=(0, 1),
intron_height=0.05, name=None, colors=None,
track_label=None):
"""
Adds bed tracks for a single set of bed features to both the bottom and
left side of the heatmap by calling ``add_bed_track()`` twice.
Parameters
----------
bed_tracks : list of dict
Each dict should represent a bed feature and could have the
following keys::
{
'chrom' : str,
'start' : int,
'end' : int,
'strand': '+' or '-'
}
The 'strand' key is optional and is only used for color-coding bed
features when ``colors`` is passed.
size : str
The size of the new axis as a percentage of the main heatmap width.
Should be passed as a string ending in '%'.
pad : float
The padding to use between the existing parts of the figure and the
newly added axis.
axis_limits : tuple of float
Axis limits for the non-genomic axis of the bed track.
intron_height : float
The height to draw each bed feature with.
name : str
Base name for the new axis. This name will be prefixed with the
orientation of the track ('vertical' or 'horizontal').
colors : dict, optional
Map from the value of the 'strand' key in the ``bed_tracks`` dicts
(usually '+' or '-') to color name for bed features with that strand
value (i.e., orientation). If not provided for a given strand or if
the bed feature doesn't have a 'strand' key the color is black by
default.
track_label : str, optional
Pass a string to label the track.
Returns
-------
list of pyplot axes
The newly added bed track axes.
"""
ax_h = self.add_bed_track(
bed_tracks, loc='bottom', size=size, pad=pad, name=name,
axis_limits=axis_limits, intron_height=intron_height, colors=colors,
track_label=track_label
)
ax_v = self.add_bed_track(
bed_tracks, loc='left', size=size, pad=pad, name=name,
axis_limits=axis_limits, intron_height=intron_height, colors=colors,
track_label=track_label
)
return [ax_h, ax_v]
[docs] def add_bed_track(self, bed_tracks, loc='bottom', size='3%', pad=0.0,
name='bed', axis_limits=(0, 1), intron_height=0.05,
colors=None, track_label=None):
"""
Adds one bed track along either the x- or y-axis of the heatmap.
Parameters
----------
bed_tracks : list of dict
Each dict should represent a bed feature and could have the
following keys::
{
'chrom' : str,
'start' : int,
'end' : int,
'strand': '+' or '-'
}
The 'strand' key is optional and is only used for color-coding bed
features when ``colors`` is passed.
loc : {'top', 'bottom', 'left', 'right'}
Which side of the heatmap to add the new bed track to.
size : str
The size of the new axis as a percentage of the main heatmap width.
Should be passed as a string ending in '%'.
pad : float
The padding to use between the existing parts of the figure and the
newly added axis.
name : str
Base name for the new axis. This name will be prefixed with the
orientation of the track ('vertical' or 'horizontal').
axis_limits : tuple of float
Axis limits for the non-genomic axis of the bed track.
intron_height : float
The height to draw each bed feature with.
colors : dict, optional
Map from the value of the 'strand' key in the ``bed_tracks`` dicts
(usually '+' or '-') to color name for bed features with that strand
value (i.e., orientation). If not provided for a given strand or if
the bed feature doesn't have a 'strand' key the color is black by
default.
track_label : str, optional
Pass a string to label the track.
Returns
-------
pyplot axis
The newly added bed track axis.
"""
# deduce orientation, either h or v, and save the correct grange
if loc in ['bottom', 'top']:
orientation = 'horizontal'
grange = self.grange_x
else:
orientation = 'vertical'
grange = self.grange_y
# create new axis
ax = self.add_margin_ax(loc=loc, size=size, pad=pad,
new_ax_name="{}_{}".format(orientation, name),
axis_limits=axis_limits)
# deduce midpoint of the non-genomic axis
midpoint = (axis_limits[0] + axis_limits[1]) / 2.
# compute track_width and track_height, assuming horizontal orientation
track_width = grange['end'] - grange['start']
# create patches for each bed
for bed in bed_tracks:
# skip bed_tracks that don't intersect the window
if not check_intersect(bed, grange):
continue
# get the color for this bed
try:
color = colors[bed['strand']]
except (TypeError, KeyError):
color = 'k'
# plot small rectangle for length of bed
intron_coords = [bed['start'], midpoint - intron_height / 2.]
intron_dims = [bed['end'] - bed['start'], intron_height]
if orientation == 'vertical':
intron_coords.reverse()
intron_dims.reverse()
ax.add_artist(mpl.patches.Rectangle(intron_coords, *intron_dims,
fc=color, ec=color))
# done looping over all bed_tracks
# write label of bed track, if specified
if track_label:
name_coords = [grange['start'] + track_width / 80, axis_limits[1]]
ha = 'left'
va = 'top'
rotation = 0
if orientation == 'vertical':
name_coords.reverse()
ha = 'right'
rotation = 270
ax.text(name_coords[0], name_coords[1], track_label, fontsize=7,
ha=ha, va=va, rotation=rotation)
# return axis for this track
return ax