/usr/lib/python2.7/dist-packages/cogent/draw/legend.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 | #!/usr/bin/env python
from __future__ import division
from cogent.core import moltype, annotation
from matplotlib.collections import PatchCollection
from matplotlib.text import Text
from matplotlib.transforms import Affine2D
from cogent.draw.rlg2mpl import Group, Drawable, figureLayout
from cogent.draw.linear import Display, DisplayPolicy
__author__ = "Peter Maxwell and Gavin Huttley"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Gavin Huttley", "Peter Maxwell", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
class Legend(Drawable):
"""A class for drawing a legend for a display policy
Arguments:
- policy: a reference to a Display policy class"""
def __init__(self, policy = DisplayPolicy):
self.policy = policy
def _makeSampleSequence(self, feature_type):
seq = moltype.DNA.makeSequence('aaaccggttt' * 7)
v = seq.addAnnotation(annotation.Feature,
feature_type, feature_type, [(2,3)])
v = seq.addAnnotation(annotation.Feature,
feature_type, feature_type, [(7,18)])
v = seq.addAnnotation(annotation.Feature,
feature_type, feature_type, [(20,70)])
return seq
def populateAxes(self, ax, columns = 3):
""" Returns the legend as a matplotlib artist
Arguments:
- columns: the number of columns of feature / representation
pairs
"""
ax.set_xlim(0, 600)
ax.set_ylim(-800, 50)
result = []
x = y = 0
for track in self.policy()._makeTrackDefns():
if track.tag is None or track.tag=="Graphs":
continue
ax.text(10, y*30, track.tag)
y -= 1
for feature in track:
seq = self._makeSampleSequence(feature)
display = Display(seq,
policy = self.policy,
min_feature_height = 10,
show_code = False,
pad = 0,)
sample = display.makeArtist()
#trans = sample.get_transform()
#offset = Affine2D()
#offset.translate(x*600+20 / columns, y*30)
sample.translate(x*600/columns+10, y*30)
ax.add_artist(sample)
ax.text(x*600/columns+90, y*30, feature)
x += 1
if x % columns == 0:
x = 0
y -= 1
if x:
x = 0
y -= 1
ax.axhline((y+.7)*30)
def makeFigure(self, margin=0, default_aspect=1.3, **kw):
kw['margin'] = margin
kw['default_aspect'] = default_aspect
(width, height), posn, kw = figureLayout(leftovers=True, **kw)
fig = self._makeFigure(width, height)
ax = fig.add_axes(posn, adjustable="datalim",
frame_on=False, xticks=[], yticks=[])
g = self.populateAxes(ax, **kw)
return fig
if __name__ == '__main__':
Legend().showFigure()
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