I have an image that I'm showing with matplotlib.
The image is generated by the following code:
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cm
labels = ['Name1', 'Name2', 'Name3', 'Name4', 'Name5', 'Name6']
data = np.array(
[[ 0.000, 0.120, 0.043, 0.094, 0.037, 0.045],
[ 0.120, 0.000, 0.108, 0.107, 0.105, 0.108],
[ 0.043, 0.108, 0.000, 0.083, 0.043, 0.042],
[ 0.094, 0.107, 0.083, 0.000, 0.083, 0.089],
[ 0.037, 0.105, 0.043, 0.083, 0.000, 2.440],
[ 0.045, 0.108, 0.042, 0.089, 2.440, 0.000]])
mask = np.tri(data.shape[0], k=-1)
data = np.ma.array(data, mask=mask) # Mask out the lower triangle of data.
fig, ax = plt.subplots(sharex=True)
im = ax.pcolor(data, edgecolors='black', linewidths=0.3)
# Format
fig = plt.gcf()
fig.set_size_inches(10, 10)
ax.set_yticks(np.arange(data.shape[0]) + 0.5, minor=False)
ax.set_xticks(np.arange(data.shape[1]) + 0.5, minor=False)
# Turn off the frame.
ax.set_frame_on(False)
ax.set_aspect('equal') # Ensure heatmap cells are square.
# Want a more natural, table-like display.
ax.invert_yaxis()
ax.yaxis.tick_right()
ax.xaxis.tick_top()
ax.set_xticklabels(labels, minor=False)
ax.set_yticklabels(labels, minor=False)
# Rotate the upper labels.
plt.xticks(rotation=90)
ax.grid(False)
ax = plt.gca()
for t in ax.xaxis.get_major_ticks():
t.tick1On = False
t.tick2On = False
for t in ax.yaxis.get_major_ticks():
t.tick1On = False
t.tick2On = False
fig.colorbar(im)
fig.savefig('out.png', transparent=False, bbox_inches='tight', pad_inches=0)
I'd like to apply a custom colormap so that values:
Any help will be greatly appreciated.
There's more than one way to do this. In your case, it's easiest to use LinearSegmentedColormap.from_list
and specify relative positions of colors as well as the colornames. (If you had evenly-spaced changes, you could skip the tuples and just do from_list('my cmap', ['blue', 'white', 'red'])
.) You'll then need to specify a manual min and max to the data (the vmin
and vmax
kwargs to imshow
/pcolor
/etc).
As an example:
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.colors import LinearSegmentedColormap
data = np.array(
[[ 0.000, 0.120, 0.043, 0.094, 0.037, 0.045],
[ 0.120, 0.000, 0.108, 0.107, 0.105, 0.108],
[ 0.043, 0.108, 0.000, 0.083, 0.043, 0.042],
[ 0.094, 0.107, 0.083, 0.000, 0.083, 0.089],
[ 0.037, 0.105, 0.043, 0.083, 0.000, 2.440],
[ 0.045, 0.108, 0.042, 0.089, 2.440, 0.000]])
mask = np.tri(data.shape[0], k=-1)
data = np.ma.masked_where(mask, data)
vmax = 3.0
cmap = LinearSegmentedColormap.from_list('mycmap', [(0 / vmax, 'blue'),
(1 / vmax, 'white'),
(3 / vmax, 'red')]
)
fig, ax = plt.subplots()
im = ax.pcolor(data, cmap=cmap, vmin=0, vmax=vmax, edgecolors='black')
cbar = fig.colorbar(im)
cbar.set_ticks(range(4)) # Integer colorbar tick locations
ax.set(frame_on=False, aspect=1, xticks=[], yticks=[])
ax.invert_yaxis()
plt.show()