When plotting heatmaps with seaborn (and correlation matrices with matplotlib) the first and the last row is cut in halve. This happens also when I run this minimal code example which I found online.

import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt

data = pd.read_csv('https://raw.githubusercontent.com/resbaz/r-novice-gapminder-files/master/data/gapminder-FiveYearData.csv')
plt.figure(figsize=(10,5))
sns.heatmap(data.corr())
plt.show()

The labels at the y axis are on the correct spot, but the rows aren’t completely there.

A few days ago, it work as intended. Since then, I installed texlive-xetex so I removed it again but it didn’t solve my problem.

Any ideas what I could be missing?

Unfortunately matplotlib 3.1.1 broke seaborn heatmaps; and in general inverted axes with fixed ticks.
This is fixed in the current development version; you may hence

• revert to matplotlib 3.1.0
• use matplotlib 3.1.2 or higher
• set the heatmap limits manually (ax.set_ylim(bottom, top) # set the ylim to bottom, top)

Its a bug in the matplotlib regression between 3.1.0 and 3.1.1 You can correct this by:

import seaborn as sns
df_corr = someDataFrame.corr()
ax = sns.heatmap(df_corr, annot=True) #notation: "annot" not "annote"
bottom, top = ax.get_ylim()
ax.set_ylim(bottom + 0.5, top - 0.5)

Fixed using the above and setting the heatmap limits manually.

First

ax = sns.heatmap(...

checked the current axes with

ax.get_ylim()
(5.5, 0.5)

Fixed with

ax.set_ylim(6.0, 0)

I solved it by adding this line in my code, with matplotlib==3.1.1:

ax.set_ylim(sorted(ax.get_xlim(), reverse=True))

NB. The only reason this works is because the x-axis isn’t changed, so use at your own risk with future mpl versions

matplotlib 3.1.2 is out – It is available in the Anaconda cloud via conda-forge but I was not able to install it via conda install. The manual alternative worked: Download matplotlib 3.1.2 from github and install via pip

 % curl https://codeload.github.com/matplotlib/matplotlib/tar.gz/v3.1.2 --output matplotlib-3.1.2.tar.gz
 % pip install matplotlib-3.1.2.tar.gz

It happens with matplotlib version 3.1.1 as suggested by importanceofbeingernest

Following solved my problem

pip install matplotlib==3.1.0

rustyDev is right about conda-forge, but I did not need to do a manual pip install from a github download. For me, on Windows, it worked directly. And the plots are all nice again.

https://anaconda.org/conda-forge/matplotlib

conda install -c conda-forge matplotlib

optional points, not needed for the answer:

Afterwards, I tried other steps, but they are not needed: In conda prompt: conda search matplotlib –info showed no new version info, the most recent info was for 3.1.1. Thus I tried pip using pip install matplotlib==3.1.2 But pip says “Requirement already satisfied”

Then getting the version according to medium.com/@rakshithvasudev/… python - import matplotlib - matplotlib.__version__ shows that 3.1.2 was successfully installed

Btw, I had this error directly after updating Spyder to v4.0.0. The error was in a plot of a confusion matrix. This was mentioned already some months ago. stackoverflow.com/questions/57225685/… which is already linked to this seaborn question.

conda install matplotlib=3.1.0

This worked for me and downgraded matplotlib from 3.1.1 to 3.1.0 and the heatmaps started to behave correctly

I solved this problem with the following code: