How to specify linewidth in Seaborn's clustermap dendrograms

Question

Normally I would increase matplotlib\'s global linewidths by editing the matplotlib.rcParams. This seems to work well directly with SciPy\'s dendrogram implementation but not wi

Answer 1

for newer versions of seaborn (tested with 0.7.1, 0.9.0), the lines are in a LineCollection, rather than by themselves. So their width can be changed as follows:

import seaborn as sns
import matplotlib.pyplot as plt

# load data and make clustermap
df = sns.load_dataset('iris')
g = sns.clustermap(df[['sepal_length', 'sepal_width']])

for a in g.ax_row_dendrogram.collections:
    a.set_linewidth(10)

for a in g.ax_col_dendrogram.collections:
    a.set_linewidth(10)

Answer 2

This has now been addressed in a more robust way by the following merged pull request https://github.com/mwaskom/seaborn/pull/1935. I'm assuming it will be included in the release after v0.9.0.

You can control the LineCollection properties of the dendrogram by using the tree_kws parameter.

For example:

>>> import seaborn as sns
>>> iris = sns.load_dataset("iris")
>>> species = iris.pop("species")
>>> g = sns.clustermap(iris, tree_kws=dict(linewidths=1.5, colors=(0.2, 0.2, 0.4))

Would create a clustermap with 1.5 pt thick lines for the tree in an alternative dark purple color.

Answer 3

There may be an easier way to do it, but this seems to work:

import matplotlib
import seaborn as sns; sns.set()

flights = sns.load_dataset("flights")
flights = flights.pivot("month", "year", "passengers")
g = sns.clustermap(flights)
for l in g.ax_row_dendrogram.lines:
        l.set_linewidth(10)
for l in g.ax_col_dendrogram.lines:
        l.set_linewidth(10)

Edit This no longer works in Seaborn v. 0.7.1 (and probably some earlier versions as well); g.ax_col_dendrogram.lines now returns an empty list. I couldn't find a way to increase line width and I ended up temporarily modifying the Seaborn module. In file matrix.py, function class _DendrogramPlotter, the linewidth is hard-coded as 0.5; I modified it to 1.5:

line_kwargs = dict(linewidths=1.5, colors='k')

This worked but obviously isn't a very sustainable approach.