Question

This seems like a simple task or a repeat, but bear with me– I’ve searched for a little while and haven’t found any easy answers.

I have a scatterplot that I would like to display as a heatmap. My values look like this:

{ (3, 3): 1.7314, (3,4):-6.99, (4,3):-17.3, (4, 4):-100.0 }

I would like to display a matrix starting with cell (3,3), which has a brightness of 1.7314, etc.

I have found several questions and answers regarding situations where you give lists of two dimensional tuples (X, Y) and the Z value (the intensity) for each point (x,y,z) is created by the number of occurrences around (x, y).

I have also used imshow to draw such a plot, but for imshow you drop the (3,3), etc. So things can be shifted strangely. One option is to use imshow and then manually adjust the axis labels afterward. But I feel like someone must have solved this before without hacking pylab too much.

What is the best way to do this?

Answer 1

Ok, let’s try an easy example using your sample data:

import numpy as np
from pylab import * 

data = { (3, 3): 1.7314, (3,4):-6.99, (4, 3):-17.3, (4, 4):-100.0 }
matrix = np.zeros((5, 5))
for (x, y), z in data.items():
    matrix[y,x] = z

imshow(matrix[3:, 3:], origin='lower', interpolation='none', extent=[2.5, 4.5, 2.5, 4.5])
show()

As you see, you can control the axes by specifying the limits using extent. The default (if None) would be (-0.5, numcols-0.5, -0.5, numrows-0.5) (left, right, bottom, top) if you specify you want the origin in the lower part, for the Y axis.

Also, interpolation='none' is important for your case.