import numpy as np
import matplotlib
matplotlib.use('Agg')
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['svg.fonttype'] = 'none'
import matplotlib.colors as pltcolors
old_settings = np.seterr(all='ignore')
[docs]def plot_single(ax, ma, average_type, color, label, plot_type='simple'):
"""
Adds a line to the plot in the given ax using the specified method
Parameters
----------
ax : matplotlib axis
matplotlib axis
ma : numpy array
numpy array The data on this matrix is summarized according
to the `average_type` argument.
average_type : str
string values are sum mean median min max std
color : str
a valid color: either a html color name, hex
(e.g #002233), RGB + alpha tuple or list or RGB tuple or list
label : str
label
plot_type: str
type of plot. Either 'se' for standard error, 'std' for
standard deviation, 'overlapped_lines' to plot each line of the matrix,
fill to plot the area between the x axis and the value or None, just to
plot the average line.
Returns
-------
ax
matplotlib axis
Examples
--------
>>> import matplotlib.pyplot as plt
>>> import os
>>> fig = plt.figure()
>>> ax = fig.add_subplot(111)
>>> matrix = np.array([[1,2,3],
... [4,5,6],
... [7,8,9]])
>>> ax = plot_single(ax, matrix -2, 'mean', color=[0.6, 0.8, 0.9], label='fill light blue', plot_type='fill')
>>> ax = plot_single(ax, matrix, 'mean', color='blue', label='red')
>>> ax = plot_single(ax, matrix + 5, 'mean', color='red', label='red', plot_type='std')
>>> ax = plot_single(ax, matrix + 10, 'mean', color='#cccccc', label='gray se', plot_type='se')
>>> ax = plot_single(ax, matrix + 20, 'mean', color=(0.9, 0.5, 0.9), label='violet', plot_type='std')
>>> ax = plot_single(ax, matrix + 30, 'mean', color=(0.9, 0.5, 0.9, 0.5), label='violet with alpha', plot_type='std')
>>> leg = ax.legend()
>>> plt.savefig("/tmp/test.pdf")
>>> plt.close()
>>> fig = plt.figure()
>>> os.remove("/tmp/test.pdf")
"""
summary = np.__getattribute__(average_type)(ma, axis=0)
# only plot the average profiles without error regions
x = np.arange(len(summary))
ax.plot(x, summary, color=color, label=label, alpha=0.9)
if plot_type == 'fill':
pass
ax.fill_between(x, summary, facecolor=color, alpha=0.6, edgecolor='none')
if plot_type in ['se', 'std']:
if plot_type == 'se': # standard error
std = np.std(ma, axis=0) / np.sqrt(ma.shape[0])
else:
std = np.std(ma, axis=0)
alpha = 0.2
# an alpha channel has to be added to the color to fill the area
# between the mean (or median etc.) and the std or se
f_color = pltcolors.colorConverter.to_rgba(color, alpha)
ax.fill_between(x, summary, summary + std, facecolor=f_color, edgecolor='none')
ax.fill_between(x, summary, summary - std, facecolor=f_color, edgecolor='none')
ax.set_xlim(0, max(x))
return ax
[docs]def getProfileTicks(hm, referencePointLabel, startLabel, endLabel):
"""
returns the position and labelling of the xticks that
correspond to the heatmap
"""
w = hm.parameters['bin size']
b = hm.parameters['upstream']
a = hm.parameters['downstream']
try:
c = hm.parameters['unscaled 5 prime']
except:
c = 0
try:
d = hm.parameters['unscaled 3 prime']
except:
d = 0
m = hm.parameters['body']
tickPlotAdj = 0.5
if b < 1e5:
quotient = 1000
symbol = 'Kb'
else:
quotient = 1e6
symbol = 'Mb'
if m == 0:
xticks = [(k / w) - tickPlotAdj for k in [0, b, b + a]]
xtickslabel = ['{0:.1f}'.format(-(float(b) / quotient)),
referencePointLabel,
'{0:.1f}{1}'.format(float(a) / quotient, symbol)]
else:
xticks_values = [0]
xtickslabel = []
# only if upstream region is set, add a x tick
if b > 0:
xticks_values.append(b)
xtickslabel.append('{0:.1f}'.format(-(float(b) / quotient)))
xtickslabel.append(startLabel)
# set the x tick for the body parameter, regardless if
# upstream is 0 (not set)
if c > 0:
xticks_values.append(b + c)
xtickslabel.append("")
if d > 0:
xticks_values.append(b + c + m)
xtickslabel.append("")
xticks_values.append(b + c + m + d)
xtickslabel.append(endLabel)
if a > 0:
xticks_values.append(b + c + m + d + a)
xtickslabel.append('{0:.1f}{1}'.format(float(a) / quotient, symbol))
xticks = [(k / w) - tickPlotAdj for k in xticks_values]
return xticks, xtickslabel