CODEWITHSUNDEEP
pythonmatplotlibseabornheatmap
Flops
Flops

Reputation: 1523

First and last row cut in half of heatmap plot

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()

And get this result (I am not allowed to embed images yet) 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?

Upvotes: 142

Views: 60287

Answers (10)

Vinod Kumar Chauhan
Vinod Kumar Chauhan

Reputation: 748

As @ImportanceOfBeingErnest mentioned, this issue is due to broken seaborn heatmaps in a specific version of matplotlib so simple solution to this problem is to upgrade matplotlib as follows:

pip install --upgrade matplotlib

Upvotes: -2

AAKANKSHA DUGGAL
AAKANKSHA DUGGAL

Reputation: 43

Downgrade your matplotlib

!pip install matplotlib==3.1.0

and add this line to your plot code :

ax[i].set_ylim(sorted(ax[i].get_xlim(), reverse=True))

Upvotes: 1

Super Mario
Super Mario

Reputation: 939

Worked for me:

b, t = plt.ylim()
b += 0.5
t -= 0.5
custom_ylim = (b, t)
plt.setp(axes, ylim=custom_ylim)

Upvotes: 1

ImportanceOfBeingErnest
ImportanceOfBeingErnest

Reputation: 339310

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)

Upvotes: 122

Magnus Berg Sletfjerding
Magnus Berg Sletfjerding

Reputation: 326

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

Upvotes: 6

questionto42
questionto42

Reputation: 9552

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.

Upvotes: 0

rustyDev
rustyDev

Reputation: 195

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

Upvotes: 3

purushotam radadia
purushotam radadia

Reputation: 49

It happens with matplotlib version 3.1.1 as suggested by importanceofbeingernest

Following solved my problem

pip install matplotlib==3.1.0

Upvotes: 0

Nikhil Pakki
Nikhil Pakki

Reputation: 981

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)

Upvotes: 98

lbarbus
lbarbus

Reputation: 259

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)

Upvotes: 25

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