Shading specific "pixels" a different color in matplotlib's pcolormesh

Question

I have a heatmap that I plot with pcolormesh:

import numpy as np
import matplotlib.pyplot as plt

# generate random array
array = np.random.rand(10,10)
x = np.arange(0,10)
y = np.arange(0,10)

fig, ax = plt.subplots(nrows=1,ncols=1)
colormesh = ax.pcolormesh(x,y,array)
ax.set_xticks(x)
ax.set_yticks(y)
cb_ax = fig.add_axes([0.93, 0.1, 0.02, 0.8])
cbar = fig.colorbar(colormesh,cax=cb_ax)
colormesh.set_clim(0,1)
plt.show()

I want to select a few pixels and shade them another color that is different from those in the colorbar. Say I set the values of these pixels to -1:

# chose the pixels to shade
array[5,5] = -1
array[0,7] = -1

I don’t want to set the colorbar limits from -1 to 1, as there is no value in the range (-1,0) and this only compresses the range of colors available for the range [0,1].

With this setup, is there a way for me to selectively color those pixels, say, red?

Notes:

I’m using pcolormesh and not imshow because in the original data x and y are not equally spaced.
I don’t want to add a dot on top of the said pixels like in this answer, but rather want to shade the whole pixel red.

Asked By: sodiumnitrate

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Source

Answer 1

You can use a color map with the under color set to red. The vmin and vmax define the range of the normal colors. Values smaller than vmin will get the under color (the default under color is the same as the lowest color in the colorbar).

Instead of under (or over), you can also set a bad color for values that are NaN or infinity.

'viridis' is matplotlib’s default colormap.

import numpy as np
import matplotlib.pyplot as plt

# generate random array
array = np.random.rand(10, 10)
x = np.arange(0, 10)
y = np.arange(0, 10)
cmap = plt.get_cmap('viridis').copy()
cmap.set_under('red')

fig, ax = plt.subplots(nrows=1, ncols=1)
# chose the pixels to shade
array[5, 5] = -1
array[0, 7] = -1
colormesh = ax.pcolormesh(x, y, array, vmin=0, vmax=1, cmap=cmap)
ax.set_xticks(x)
ax.set_yticks(y)
cbar = fig.colorbar(colormesh)
plt.show()

Answered By: JohanC

Shading specific "pixels" a different color in matplotlib's pcolormesh

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