5 Best Ways to Deal with NaN Values While Plotting a Boxplot Using Python Matplotlib

Rate this post

πŸ’‘ Problem Formulation: When working with real-world datasets in Python, it’s common to encounter NaN (Not a Number) values. Plotting functions like boxplots in Matplotlib can be problematic when NaN values are present, as they can distort the visualization or result in errors. The goal is to manage or remove NaN values in a way that still yields an accurate and informative boxplot. Let’s explore methods to deal with this issue effectively.

Method 1: Remove NaN Values Before Plotting

An approach to handle NaN values when plotting with Matplotlib is to remove them from the dataset. This can be done using the dropna() function from Pandas, ensuring that the boxplot only includes valid numerical data.

Here’s an example:

import matplotlib.pyplot as plt
import pandas as pd
import numpy as np

# Create data with NaN values
data = pd.Series([1, 2, np.nan, 4, 5, np.nan, 7, 8])

# Remove NaN values
cleaned_data = data.dropna()

# Plot the boxplot
plt.boxplot(cleaned_data)
plt.show()

The output will display a boxplot with the NaN values excluded.

In the code example, we first generate a Pandas Series containing NaN values among valid numeric entries. The dropna() function is used to filter out these NaN values, creating a new data set cleaned_data. This clean dataset is then passed to Matplotlib’s boxplot() function to generate a boxplot without any NaN interference.

Method 2: Replace NaN Values with a Defined Statistic

Instead of removing NaN values, another method is to replace them with a representative statistic, such as the mean or median of the dataset. This method allows for maintaining the original size of the dataset and can be accomplished using the fillna() function in Pandas.

Here’s an example:

import matplotlib.pyplot as plt
import pandas as pd
import numpy as np

# Create data with NaN values
data = pd.Series([1, 2, np.nan, 4, 5, np.nan, 7, 8])

# Replace NaN values with the mean of the dataset
filled_data = data.fillna(data.mean())

# Plot the boxplot
plt.boxplot(filled_data)
plt.show()

The output is a boxplot where NaN values have been replaced with the mean of the remaining data.

This snippet demonstrates replacing NaN values with the mean of the non-NaN values in the series. The fillna() function is given data.mean() which calculates the mean, providing a straightforward way to deal with missing data points in a way that might preserve trends in the dataset without dropping data points.

Method 3: Use Matplotlib’s NaN Handling

Matplotlib’s boxplot function has a mechanism to handle NaN values internally. By default, it ignores NaNs when plotting. This method requires no additional steps from the user, allowing for a quick and direct plotting experience.

Here’s an example:

import matplotlib.pyplot as plt
import numpy as np

# Create data with NaN values
data = np.array([1, 2, np.nan, 4, 5, np.nan, 7, 8])

# Plot the boxplot - NaN values are ignored by default
plt.boxplot(data)
plt.show()

The plotted boxplot automatically excludes the NaN values.

In this example, we feed the dataset with NaN values directly into Matplotlib’s boxplot() function. The NaN values are internally handled and ignored, ensuring the plot renders without error or distortion.

Method 4: Use Seaborn, Which Ignores NaN Values

Seaborn, a statistical data visualization library in Python, which is built on top of Matplotlib, ignores NaN values by default when plotting. Seaborn offers a more high-level interface and additional features which can be an advantage.

Here’s an example:

import seaborn as sns
import numpy as np

# Create data with NaN values
data = np.array([1, 2, np.nan, 4, 5, np.nan, 7, 8])

# Plot the boxplot with Seaborn
sns.boxplot(data=data)

The Seaborn boxplot will present a plot without the NaN values affecting it.

With Seaborn’s boxplot function, no preliminary cleaning of NaN values is needed. This example showcases the ease with which a boxplot can be created with Seaborn directly from a dataset containing NaN values.

Bonus One-Liner Method 5: Use np.nan_to_num()

If you want a quick one-liner solution, you can use NumPy’s nan_to_num() function. It replaces NaN values with zeroes (or any other specified number), thus maintaining the distribution of data points.

Here’s an example:

import matplotlib.pyplot as plt
import numpy as np

# Create data with NaN values
data = np.array([1, 2, np.nan, 4, 5, np.nan, 7, 8])

# Replace NaN values with 0 and plot
plt.boxplot(np.nan_to_num(data))
plt.show()

A boxplot will be shown where NaN values have been replaced with zero.

Utilizing NumPy’s nan_to_num(), we can convert NaN values to zero in the dataset with a simple one-liner code. This method is best suited for cases where the distribution is not severely affected by the introduction of zeros.

Summary/Discussion

  • Method 1: Removing NaN Values. Strengths: Simple and prevents misleading data points. Weaknesses: Can result in loss of data, affecting the distribution.
  • Method 2: Replacing NaN with Statistics. Strengths: Maintains data size and can preserve general trends. Weaknesses: Potentially introduces bias based on the choice of statistic.
  • Method 3: Matplotlib’s NaN Handling. Strengths: No extra code required. Weaknesses: Similar to removal, data points are lost.
  • Method 4: Using Seaborn. Strengths: Built-in functionality with advanced plotting options. Weaknesses: Excludes NaN values, similar to Matplotlib.
  • Bonus Method 5: np.nan_to_num() Function. Strengths: Quick and simple. Weaknesses: Adding zeros could potentially skew data distribution.