Matplotlib and numpy histogram2d axis issue

Question

I'm struggling to get the axis right:

I've got the x and y values, and want to plot them in a 2d histogram (to examine correlation). Why do I get a histogram with limits from 0-9 on each axis? How do I get it to show the actual value ranges?

This is a minimal example and I would expect to see the red "star" at (3, 3):

import numpy as np
import matplotlib.pyplot as plt

x = (1, 2, 3, 4, 5, 1, 2, 3, 4, 5, 3)
y = (1, 2, 3, 4, 5, 1, 2, 3, 4, 5, 3)
xedges = range(5)
yedges = range(5)
H, xedges, yedges = np.histogram2d(y, x)
im = plt.imshow(H, origin='low')
plt.show()

Answer 1

I think the problem is twofold:

Firstly you should have 5 bins in your histogram (it's set to 10 as default):

H, xedges, yedges = np.histogram2d(y, x,bins=5)

Secondly, to set the axis values, you can use the extent parameter, as per the histogram2d man pages:

im = plt.imshow(H, interpolation=None, origin='low',
                extent=[xedges[0], xedges[-1], yedges[0], yedges[-1]])

Answer 2

If I understand correctly, you just need to set interpolation='none'

import numpy as np
import matplotlib.pyplot as plt

x = (1, 2, 3, 4, 5, 1, 2, 3, 4, 5, 3)
y = (1, 2, 3, 4, 5, 1, 2, 3, 4, 5, 3)
xedges = range(5)
yedges = range(5)
H, xedges, yedges = np.histogram2d(y, x)
im = plt.imshow(H, origin='low', interpolation='none')

Does that look right?