CODEWITHSUNDEEP
python-3.xcommandjupyter-notebookgraphvizdecision-tree
Rafa.Rugamas
Rafa.Rugamas

Reputation: 87

Can't display graphviz tree in Jupyter Notebook

I'm trying to display a decision tree in Jupyter Notebook and I keep receiving the message: 

CalledProcessError: Command '['dot.bat', '-Tsvg']' returned non-zero exit status 1

I'm using the following code: 

from sklearn.datasets import load_iris 
from sklearn import tree
import graphviz
from IPython.display import SVG
iris = load_iris()
clf = tree.DecisionTreeClassifier()
fitted_clf = clf.fit(iris.data, iris.target)
graph = graphviz.Source(tree.export_graphviz(fitted_clf, 
                               feature_names = iris.feature_names,
                               class_names = iris.target_names, 
                               filled = True, rounded = True, 
                               special_characters = True))
SVG(graph.pipe(format='svg'))

The Exception is raised in the last line when I try to use 'pipe'. I also tried: 

graph.format = 'png'
graph.render('example')

instead of pipe but i keep on raising a similar exception: 

CalledProcessError: Command '['dot.bat', '-Tpng', '-O', 'example']' returned non-zero exit status 1

Any idea of what is causing that behaviour? and how can I fix it?

(I'm using Python 3.5.2, sklearn 0.17.1, graphviz 0.8.2 and IPython 6.4.0)

Upvotes: 4

Views: 9202

Answers (2)

Paul-Armand Verhaegen
Paul-Armand Verhaegen

Reputation: 547

Installing graphviz xorg-libxrender xorg-libxpm from conda-forge repo, and the python bindings from pip usually solves this for me.

conda install -c conda-forge graphviz xorg-libxrender xorg-libxpm
pip install graphviz

Do not forget to uninstall the previously installed packages first.

Edit: please try conda install python-graphviz instead of pip install graphviz first, as proposed in the comment below. Mixing conda and pip solved it for me multiple times, but should only be used if pure pip or conda installs fail.

Upvotes: 3

Yann Dubois
Yann Dubois

Reputation: 1345

Paul-Armand's answer should work if you are working with conda. If not then you have to run : 

brew install graphviz
pip install graphviz

In case you get a warning saying that graphviz is already installed but not linked then follow the instruction to link it. I.e brew link graphviz (or brew link --overwrite graphviz if the former gives an error).

The reason it works in conda without brew is that conda install graphviz actually installs the c++ library not the python one.

Upvotes: 0

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