Bug report for matplotlib

plot_results.py

import numpy as np

import matplotlib
from matplotlib import pyplot as plt

from matplotlib.collections import PatchCollection
from matplotlib import patches

"""
This code is meant to analyse where telomeres and centromers are most often
found in our experiments.
"""

save = True

X = np.load('X.npy')
im = np.load('im.npy')
a = np.load('im_binned.npy')

patch = []

art = patches.Circle((1900, 1200), 300, ec="none")
patch.append(art)

art = patches.Circle((1200, 1200), 1000, ec="none")
patch.append(art)

font = "sans-serif"

fig = plt.figure(figsize=(6, 6))
ax = fig.add_subplot(111)

ax.set_xlim((-1.2, 1.2))
ax.set_ylim((-1.2, 1.2))

# add a the nucleolus
plt.text(0.7, 0 - 0.15, "Nucleolus", ha="center",
        family=font, size=14)

nucleolus = patches.Circle((0.7, 0), 0.3, ec="none")
nucleus = patches.Circle((0, 0), 1, ec="none")

collection = PatchCollection([nucleolus, nucleus],
                             match_original=False, linewidth=2,
                             linestyle='--', facecolor='None')
ax.add_collection(collection)
ax.scatter(X[:, 0], X[:, 1], alpha=0.2)
ax.set_axis_off()
if save:
    fig.savefig('im1.png')

fig = plt.figure(figsize=(6, 6))
ax = fig.add_subplot(111)

ax.set_xlim((0, 2400))
ax.set_ylim((0, 2400))

# add a the nucleolus
plt.text(1900, 1200, "Nucleolus", ha="center",
        family=font, size=14)

collection = PatchCollection(patch, match_original=False, linewidth=2,
                             linestyle='--', facecolor='None')
ax.add_collection(collection)
ax.matshow(a)
ax.set_axis_off()
if save:
    fig.savefig('im2.png')


fig = plt.figure(figsize=(6, 6))
ax = fig.add_subplot(111)

ax.set_xlim((0, 2400))
ax.set_ylim((0, 2400))

plt.text(1900, 1200, "Nucleolus", ha="center",
        family=font, size=14)

ax.add_collection(collection)
ax.matshow(im)
ax.set_axis_off()
if save:
    fig.savefig('im3.png')

plt.show()