How to Make a Violin plot in Python using Matplotlib and Seaborn

In this Python data visualization tutorial, we will learn how to create a violin plot in Python with Matplotlib and Seaborn. We can carry out several techniques for visualizing data (see the post 9 Data Visualization Techniques You Should Learn in Python for some examples). Violin plots combine both the box plot and the histogram. In the next section, you will get a brief overview of the content of this blog post.

Table of Contents

• Outline
• Requirements
• Example Data
• How to Make a Violin Plot in Python with Matplotlib
• Grouped Violin Plot in Python with Matplotlib
• Displaying Median in the Violin Plot Created with Matplotlib
• How to Create a Violin Plot in Python with Seaborn
• Grouped Violin Plot in Python using Seaborn
• Grouped Violin Plot in Seaborn with Split Violins
• Horizontal Violin Plot in Python with Seaborn
• Conclusion
• Resources

Outline

Before we get into the details of creating a violin plot in Python, we will look at what is needed to follow this Python data visualization tutorial. We will answer some questions when we have what we need (e.g., learn what a violin plot is). In the following sections, we will get into the practical parts. We will learn how to use 1) Matplotlib and 2) Seaborn to create a violin plot in Python.

Requirements

First, you need to have Python 3 installed to follow this post. Second, to use both Matplotlib and Seaborn you need to install these two excellent Python packages. Now, you can install Python packages using both Pip and conda. The latter is if you have Anaconda (or Miniconda) Python distribution. Note, Seaborn requires that Matplotlib is installed, so if you, for example, want to try both packages to create violin plots in Python, you can type pip install seaborn. This will install Seaborn, Matplotlib, and other dependencies (e.g., NumPy and SciPy). Oh, we are also going to read the example data using Pandas. Pandas can, of course, also be installed using pip.

Example Data

In this post, we are going to work with a fake dataset. This dataset can be downloaded here and is data from a Flanker task created with OpenSesame. Of course, the experiment was never actually run to collect the current data. Here is how we read a CSV file with Pandas:

import pandas as pd

data = 'https://raw.githubusercontent.com/marsja/jupyter/master/flanks.csv'

df = pd.read_csv(data, index_col=0)
df.head()Code language: Python (python)

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Now, we can calculate descriptive statistics in Python using Pandas describe():

df.loc[:, 'TrialType':'ACC'].groupby(by='TrialType').describe()Code language: Python (python)

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In the code chunk above, we used loc to slice the Pandas dataframe. This as we did not want to calculate summary statistics on the SubID. Furthermore, we used Pandas groupby to group the data by condition (i.e., “TrialType”). Now that we have some data, we will continue exploring the data by creating a violin plot using 1) Matplotlib and 2) Seaborn.

How to Make a Violin Plot in Python with Matplotlib

Here is how to create a violin plot with the Python package Matplotlib:

import matplotlib.pyplot as plt

plt.violinplot(df['RT'])Code language: Python (python)

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n the code above, we used the violinplot() method and used the dataframe as the only parameter. Furthermore, using the brackets, we selected only the response time (i.e. the “RT” column). Now, as we know, there are two conditions in the dataset and, therefore, we should create one violin plot for each condition. In the next example, we will subset the data and create violin plots, using matplotlib, for each condition.

Grouped Violin Plot in Python with Matplotlib

One way to create a violin plot for the different conditions (grouped) is to subset the data:

# Subsetting using Pandas query():
congruent = df.query('TrialType == "congruent"')['RT']
incongruent = df.query('TrialType == "incongruent"')['RT']

fig, ax = plt.subplots()

inc = ax.violinplot(incongruent)
con = ax.violinplot(congruent)
                       
fig.tight_layout()Code language: Python (python)

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We can see some overlap in the distributions, but they seem slightly different. Furthermore, we can see that iqr is a bit different—especially the tops. However, we do not know which color represents which. However, from the descriptive statistics earlier, we can assume that the blue one is incongruent. Note we also know this because that is the first one we created.

We can make this plot easier to read by using some more methods. In the following code chunk, we will create a list of the data, add ticks labels to the plot, and set (two) ticks to the plot.

# Combine data
plot_data = list([incongruent, congruent])

fig, ax = plt.subplots()

xticklabels = ['Incongruent', 'Congruent']
ax.set_xticks([1, 2])
ax.set_xticklabels(xticklabels)

ax.violinplot(plot_data)Code language: Python (python)

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Notice how we now get the violin plots side by side instead. In the next example, we are going to add the median to the plot using the showmedians parameter.

Displaying Median in the Violin Plot Created with Matplotlib

Here is how we can show the median in the violin plots we create with the Python library matplotlib:

fig, ax = plt.subplots()

xticklabels = ['Incongruent', 'Congruent']
ax.set_xticks([1, 2])
ax.set_xticklabels(xticklabels)

ax.violinplot(plot_data, showmedians=True)Code language: Python (python)

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In the next section, we will start working with Seaborn to create a violin plot in Python. This package is built as a wrapper to Matplotlib and is a bit easier to work with. First, we will start by creating a simple violin plot (the same as the first example using Matplotlib). Second, we will create grouped violin plots as well.

How to Create a Violin Plot in Python with Seaborn

Here is how we can create a violin plot in Python using Seaborn:

import seaborn as sns

sns.violinplot(y='RT', data=df)Code language: JavaScript (javascript)

In the code chunk above, we imported seaborn as sns. This enables us to use a range of methods, and, in this case, we created a violin plot with Seaborn. Notice how we set the first parameter as the dependent variable and the second as our Pandas dataframe.

Again, we know that there are two conditions and, therefore, in the next example, we will use the x parameter to create violin plots for each group (i.e., conditions).

Grouped Violin Plot in Python using Seaborn

To create a grouped violin plot in Python with Seaborn, we can use the x parameter:

sns.violinplot(y='RT', x="TrialType",
              data=df)Code language: Python (python)

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This violin plot is now easier to read than the one we created using Matplotlib. We get a violin plot for each group/condition, side by side, with axis labels. All this by using a single Python method! If we have further categories, we can also use the split parameter to get KDEs for each category split. Let’s see how we do that in the next section.

Grouped Violin Plot in Seaborn with Split Violins

Here is how we can use the split parameter, and set it to True to get a KDE for each level of a category:

sns.violinplot(y='RT', x="TrialType", split=True, hue='ACC',
              data=df)Code language: Python (python)

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In the next and final example, we are going to create a horizontal violin plot in Python with Seaborn and the orient parameter.

Horizontal Violin Plot in Python with Seaborn

Here is how we use the orient parameter to get a horizontal violin plot with Seaborn:

sns.violinplot(y='TrialType', x="RT", orient='h',
              data=df)Code language: Python (python)

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Notice how we also flipped the y and x parameters. That is, we now have the dependent variable (“RT”) as the x parameter. If we want to save a plot, whether created with Matplotlib or Seaborn, we might want to e.g. change the Seaborn plot size and add or change the title and labels. Here is a code example of customizing a Seaborn violin plot:

import seaborn as sns
import matplotlib.pyplot as plt

fig = plt.gcf()

# Change seaborn plot size
fig.set_size_inches(10, 8)

# Increase font size
sns.set(font_scale=1.5)

# Create the violin plot
sns.violinplot(y='RT', x='TrialType',
              data=df)

# Change Axis labels:
plt.xlabel('Condition')
plt.ylabel('Response Time (MSec)')
plt.title('Violin Plot Created in Python')Code language: Python (python)

In the above code chunk, we have a fully working example of creating a violin plot in Python using Seaborn and Matplotlib. Now, we start by importing the needed packages. After that, we make a new figure with plt.gcf(). In the following code lines, we change the size of 1) the plot and 2) the font. Now, we are creating the violin plot and changing the x- and y-axis labels. Finally, the title is added to the plot.

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For more data visualization tutorials:

• How to Plot a Histogram with Pandas in 3 Simple Steps
• 9 Python Data Visualization Examples (Video)
• How to Make a Scatter Plot in Python using Seaborn
• Seaborn Line Plots: A Detailed Guide with Examples (Multiple Lines)

Conclusion

In this post, you have learned how to make a violin plot in Python using the packages Matplotlib and Seaborn. First, you learned a bit about a violin plot and how to create single and grouped violin plots in Python with 1) Matplotlib and 2) Seaborn.

Resources

Here are some more Python tutorials you may find helpful:

• Coefficient of Variation in Python with Pandas & NumPy
• How to use Square Root, log, & Box-Cox Transformation in Python
• Python Scientific Notation & How to Suppress it in Pandas & NumPy
• How to Perform Mann-Whitney U Test in Python with Scipy and Pingouin
• Find the Highest Value in Dictionary in Python
• How to use Python to Perform a Paired Sample T-test
• Your Guide to Reading Excel (xlsx) Files in Python