Custom cluster colors of SciPy dendrogram in Python (link_color_func?)

Question

I want to color my clusters with a color map that I made in the form of a dictionary (i.e. {leaf: color}).

I\'ve tried following https://joernhees.de/

Answer 1

Two-liner for applying custom colormap to cluster branches:

import matplotlib as mpl
from matplotlib.pyplot import cm
from scipy.cluster import hierarchy

cmap = cm.rainbow(np.linspace(0, 1, 10))
hierarchy.set_link_color_palette([mpl.colors.rgb2hex(rgb[:3]) for rgb in cmap])

You can then replace rainbow by any cmap and change 10 for the number of cluster you want.