Description
Pandas version checks
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I have checked that this issue has not already been reported.
-
I have confirmed this bug exists on the latest version of pandas.
-
I have confirmed this bug exists on the main branch of pandas.
Reproducible Example
#%%
import pandas as pd
df = pd.DataFrame({"i": [1, 2, 3],
"g1": ["a", "b", "b"],
"g2": ["x", None, None],
})
df.pivot_table(index="g1",
columns="g2",
values="i",
aggfunc="count",
dropna=False, margins=True)Issue Description
The margins of a pivot_table are incorrect when the index or columns variables contains missing variables. In particular, for the variable with the missing value, the total is missing.
| g1 | x | nan | Total |
|---|---|---|---|
| a | 1.0 | 1 | |
| b | 2.0 | 2 | |
| All | 1.0 | 3 |
Expected Behavior
Margins should also be included for columns/indices with missing values.
In particular, the table should look like this
| g1 | x | nan | Total |
|---|---|---|---|
| a | 1.0 | 1 | |
| b | 2.0 | 2 | |
| All | 1.0 | 2.0 | 3 |
Installed Versions
INSTALLED VERSIONS
commit : f538741
python : 3.12.8.final.0
python-bits : 64
OS : Linux
OS-release : 6.11.0-26-generic
Version : #26~24.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Apr 17 19:20:47 UTC 2
machine : x86_64
processor : x86_64
byteorder : little
LC_ALL : None
LANG : en_US.UTF-8
LOCALE : en_US.UTF-8
pandas : 2.2.0
numpy : 1.26.4
pytz : 2025.1
dateutil : 2.9.0.post0
setuptools : 75.8.0
pip : 25.0
Cython : None
pytest : None
hypothesis : None
sphinx : 8.1.3
blosc : None
feather : None
xlsxwriter : None
lxml.etree : None
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 3.1.5
IPython : 8.22.0
pandas_datareader : None
adbc-driver-postgresql: None
adbc-driver-sqlite : None
bs4 : 4.13.0
bottleneck : None
dataframe-api-compat : None
fastparquet : None
fsspec : None
gcsfs : None
matplotlib : 3.9.4
numba : None
numexpr : None
odfpy : None
openpyxl : 3.1.4
pandas_gbq : None
pyarrow : 16.1.0
pyreadstat : None
python-calamine : None
pyxlsb : None
s3fs : None
scipy : 1.14.0
sqlalchemy : None
tables : None
tabulate : None
xarray : None
xlrd : None
zstandard : 0.23.0
tzdata : 2025.1
qtpy : 2.4.2
pyqt5 : None