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()

histogram2d

Lee · Accepted Answer · 2014-05-14 21:15:39Z

4

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]])

enter image description here

edited May 14, 2014 at 21:15

answered May 14, 2014 at 21:09

Lee

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Comments

Paul H · Accepted Answer · 2014-05-14 19:43:06Z

1

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')

enter image description here

Does that look right?

answered May 14, 2014 at 19:43

Paul H

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2 Comments

tamasgal Over a year ago

Not really, the red square is still at (5,5) and want the scales so that they're reflecting the actual data values. The red square should be at (3,3).

tacaswell Over a year ago

It is both, you need extent + interoplation='none'

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