/usr/lib/python2.7/dist-packages/cogent/draw/dinuc.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 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 | #/usr/bin/env python
"""Provides a plot for visualizing dinucleotide frequencies..
"""
from matplotlib import use, rc
from matplotlib.font_manager import FontProperties
use('Agg') #suppress graphical rendering
from matplotlib.ticker import FixedFormatter
from pylab import arange, axvline, array, plot, scatter, legend, gca, xlim, \
savefig
__author__ = "Stephanie Wilson"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Rob Knight", "Stephanie Wilson"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
rc('text', usetex=True)
rc('font', family='serif') #required to match latex text and equations
colors = ["#000000","#FF0000","#00FF00","#FFFF00",
"#CC99FF","#FFCC99","#CCFFFF","#C0C0C0",
"#6D6D6D","#2353FF","#00FFFF","#FF8800",
"#238853","#882353","#EC008C","#000099"]
axis_names= [a+b for a in 'UCAG' for b in 'UCAG']
#place to put the averages, and the genes on x axis
line_positions = arange(16)
#standard_gene_type_formats provides arguments to plot() that depend on the type
#of gene. All contents of this dict must be valid arguments and values for
#plot()!
standard_gene_type_formats = {
'hgt':{'marker':'d'},
'ribosomal':{'marker':'s'},
None:{'marker':'o'},
}
#offsets maps labels onto horizontal positions within each column. Offset of
#0.5 means it will appear in the middle of the column.
offsets = {
'hgt': 0.3,
'ribosomal':0.7,
None: 0.5
}
light_gray = '#CCCCCC' #define standard color for background lines
def dinuc_plot(data, graph_name="ADinucTester.png", title = "", \
gene_type_formats=standard_gene_type_formats, \
background_line_color=light_gray, avg_formats={},
point_formats={}):
"""Returns dinucleotide usage plot from given species data.
Data is a dict with the following structure:
{name: {gene_type: [values]}}
where name is e.g. the name of the species (will be displayed on graph),
and gene_type will be the name of the type of gene (e.g. ribosomal,
hgt, non-hgt, all).
Values should be the 16-element array obtained from calling normalize() on
the DinucUsage objects giving the DinucUsage frequencies, as fractions,
for each of the 16 dinucleotides in alphabet order (TT -> GG).
Calculates the average of each gene type on the fly and connects these
averages with lines. If you have precalculated the average, just pass it
in as a single 'gene' (the average of an array with one item will be
itself...).
avg_formats should be passable to plot(), e.g. markersize.
point_formats should be passable to scatter(), e.g. 'c'.
"""
#constructing the vertical lines
for a in line_positions:
axvline(a,ymin=0,ymax=1, color=background_line_color)
curr_color_index = 0
lines = []
labels = []
for label, gene_types in sorted(data.items()):
gene_types = data[label]
curr_color = colors[curr_color_index]
for type_label, usages in sorted(gene_types.items()):
labels.append(':'.join(map(str, [label,type_label])))
x_positions = line_positions + \
offsets.get(type_label, offsets[None])
curr_format = gene_type_formats.get(type_label, \
gene_type_formats[None])
#plot the averages...connected with a line for easier visual
avg_format = curr_format.copy()
avg_format.update(avg_formats)
avg = sum(array(usages))/len(usages)
curr_line = plot(x_positions, avg, color=curr_color,
markerfacecolor=curr_color, label=label,
**avg_format)
lines.append(curr_line)
point_format = curr_format.copy()
if len(usages) > 1: #got more than one gene: plot points
point_format.update(point_formats)
for u in usages:
scatter(x_positions, u, c=curr_color, **point_format)
#get the next color
try:
curr_color_index += 1
except IndexError: #fell off end of list -- wrap around
curr_color_index = 0
legend(lines, labels, loc='best', \
prop=FontProperties(size='smaller'))
a = gca()
a.set_yticks(arange(0,1.01,.1)) #set the yaxis labels
a.set_xticks(arange(0.5,16.5,1))
a.xaxis.set_major_formatter(FixedFormatter(axis_names))
xlim(0,16)
if graph_name is not None:
savefig(graph_name)
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