Pandas FutureWarning: DataFrame.groupby with axis=1 is deprecated

Updated: February 22, 2024 By: Guest Contributor Post a comment

The Problem

The ‘FutureWarning: DataFrame.groupby with axis=1 is deprecated’ issue in Pandas can originate from various scenarios, chiefly involving attempts to use the groupby() function along columns instead of rows. This warning signals that in future versions of Pandas, the functionality to perform grouping operations across columns (setting axis=1) will no longer be supported. Understanding and rectifying this early will prevent compatibility issues with newer versions of the library.

Solution 1: Transpose Before GroupBy

A straightforward method to resolve this issue involves transposing the DataFrame, performing the groupby() operation as usual (which now defaults to along rows, the only soon-to-be-supported mode), and then optionally transposing the result back.

  1. Transpose the DataFrame.
  2. Perform the groupby() operation.
  3. Transpose the result back if necessary.

Code Example:

import pandas as pd
df = pd.DataFrame({
    'A': [1, 2, 3],
    'B': [4, 5, 6],
    'C': [7, 8, 9]
df_T = df.T
grouped = df_T.groupby(level=0).mean()
result = grouped.T


     A    B    C
0  1.0  4.0  7.0
1  2.0  5.0  8.0
2  3.0  6.0  9.0

Note: This approach maintains the initial DataFrame structure while adapting to the upcoming change in Pandas. However, it might not be suitable for very large DataFrames due to potential performance issues related to the double transposition.

Solution 2: Use Pivot Instead

For certain use cases, particularly those involving aggregation of values across columns, converting the groupby() operation into a pivot operation can be a more appropriate solution. This avoids deprecation issues entirely by adapting the approach to fit Pandas’ recommended use cases.

  1. Identify the columns that would’ve been grouped by.
  2. Use the pivot() or pivot_table() function accordingly.
  3. Specify the index, columns, and values parameters based on your data structure.

Code Example:

import pandas as pd
df = pd.DataFrame({
    'A': ['a', 'b', 'c'],
    'B': [1, 2, 3],
    'C': [4, 5, 6]
result = df.pivot_table(index='A', columns='B', values='C', aggfunc='sum')


B    1    2    3
a    4.0  NaN  NaN
b    NaN  5.0  NaN
c    NaN  NaN  6.0

Note: Pivoting is generally more efficient than the transposing-grouping-transposing method, especially for aggregation tasks. However, it requires a solid understanding of the pivot() and pivot_table() functions and might not fit all scenarios initially intended for column-based grouping.