"""
Module for the RulerExtendableHeatmap class, which adds ruler track plotting
functionality for the extendable heatmap system.
"""
import numpy as np
from lib5c.plotters.extendable.base_extendable_heatmap import \
BaseExtendableHeatmap
[docs]class RulerExtendableHeatmap(BaseExtendableHeatmap):
"""
ExtendableHeatmap mixin class providing ruler track plotting functionality.
"""
[docs] def add_rulers(self, size='5%', pad=0.0, axis_limits=(1, 0),
ruler_tick_height=0.3, ruler_text_baseline=0.5,
no_ticks=False, fontsize=7, no_tick_precision=2):
"""
Adds a ruler track to both the bottom and left side of the heatmap by
calling ``add_ruler()`` twice.
Parameters
----------
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 ruler track.
ruler_tick_height : float
The height of the ruler ticks.
ruler_text_baseline : float
Controls how far away from the top of the new axis the text elements
(chromosome name and region size) will be drawn.
no_ticks : bool
Pass True to skip plotting ruler ticks, and instead write the start
and end coordinate of the plotted region in units of megabase pairs.
fontsize : float
The font size to use for adding labels to the ruler axis.
no_tick_precision : int
When ``no_ticks`` is True, round the start and end coordinates of
the plotted region to this many digits after the decimal.
Returns
-------
list of pyplot axes
The newly added gene ruler axes.
"""
ax_h = self.add_ruler(loc='bottom', size=size, pad=pad,
new_ax_name='h_ruler', axis_limits=axis_limits,
ruler_tick_height=ruler_tick_height,
ruler_text_baseline=ruler_text_baseline,
no_ticks=no_ticks, fontsize=fontsize,
no_tick_precision=no_tick_precision)
ax_v = self.add_ruler(loc='left', size=size, pad=pad,
new_ax_name='v_ruler', axis_limits=axis_limits,
ruler_tick_height=ruler_tick_height,
ruler_text_baseline=ruler_text_baseline,
no_ticks=no_ticks, fontsize=fontsize,
no_tick_precision=no_tick_precision)
return [ax_h, ax_v]
[docs] def add_ruler(self, loc='bottom', size='5%', pad=0.0, new_ax_name='ruler',
axis_limits=(1, 0), ruler_tick_height=0.3,
ruler_text_baseline=0.5, no_ticks=False, fontsize=7,
no_tick_precision=2):
"""
Adds one ruler track along either the x- or y-axis of the heatmap.
Parameters
----------
loc : {'top', 'bottom', 'left', 'right'}
Which side of the heatmap to add the new ruler 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.
new_ax_name : str
The name for the newly created axis.
axis_limits : tuple of float
Axis limits for the non-genomic axis of the ruler track.
ruler_tick_height : float
The height of the ruler ticks.
ruler_text_baseline : float
Controls how far away from the top of the new axis the text elements
(chromosome name and region size) will be drawn.
no_ticks : bool
Pass True to skip plotting ruler ticks, and instead write the start
and end coordinate of the plotted region in units of megabase pairs.
fontsize : float
The font size to use for adding labels to the ruler axis.
no_tick_precision : int
When ``no_ticks`` is True, round the start and end coordinates of
the plotted region to this many digits after the decimal.
Returns
-------
pyplot axis
The newly added ruler track axis.
"""
# create new axis
ax = self.add_margin_ax(loc=loc, size=size, pad=pad,
new_ax_name=new_ax_name,
axis_limits=axis_limits)
# 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
# compute tick positions
tick_positions = np.linspace(grange['start'], grange['end'], 5)
# compute track_width, assuming horizontal orientation
track_width = grange['end'] - grange['start']
if not no_ticks:
# plot ticks and labels
for i in range(1, 4):
# ticks
tick_coords = [(tick_positions[i], tick_positions[i]),
(0, ruler_tick_height)]
if orientation == 'vertical':
tick_coords.reverse()
ax.plot(*tick_coords, c='k', lw=1.25)
# labels
label_coords = [tick_positions[i], ruler_text_baseline]
ha = 'center'
va = 'top'
rotation = 0
if orientation == 'vertical':
label_coords.reverse()
ha = 'right'
va = 'center'
rotation = 270
ax.text(label_coords[0], label_coords[1],
str(int(tick_positions[i])),
fontsize=fontsize, ha=ha, va=va, rotation=rotation)
# write chromosome
chrom_coords = [grange['start'] + track_width / 80, ruler_text_baseline]
ha = 'left'
va = 'top'
rotation = 0
if orientation == 'vertical':
chrom_coords.reverse()
ha = 'right'
rotation = 270
if no_ticks:
MB_SCALE = 1e6 # to divide start and end by. Float so get decimals
chrom_str = '{chrom}:{startMb:.{prec}f}-{endMb:.{prec}f}Mb'
chrom_str = chrom_str.format(chrom=grange['chrom'],
startMb=grange['start']/MB_SCALE,
endMb=grange['end']/MB_SCALE,
prec=no_tick_precision)
else:
chrom_str = '{chrom}'.format(chrom=grange['chrom'])
ax.text(chrom_coords[0], chrom_coords[1], chrom_str, fontsize=fontsize,
ha=ha, va=va, rotation=rotation)
# write window width
width_coords = [grange['end'] - track_width / 80, ruler_text_baseline]
ha = 'right'
va = 'top'
rotation = 0
if orientation == 'vertical':
width_coords.reverse()
va = 'bottom'
rotation = 270
ax.text(width_coords[0], width_coords[1],
'%ikb' % (track_width // 1000), fontsize=fontsize, ha=ha, va=va,
rotation=rotation)
return ax