Pandas concat yields ValueError: Plan shapes are not aligned

In case it helps, I have also hit this error when I tried to concatenate two data frames (and as of the time of writing this is the only related hit I can find on google other than the source code).

I don't know whether this answer would have solved the OP's problem (since he/she didn't post enough information), but for me, this was caused when I tried to concat dataframe df1 with columns ['A', 'B', 'B', 'C'] (see the duplicate column headings?) with dataframe df2 with columns ['A', 'B']. Understandably the duplication caused pandas to throw a wobbly. Change df1 to ['A', 'B', 'C'] (i.e. drop one of the duplicate columns) and everything works fine.

I recently got this message, too, and I found like user @jason and @user3805082 above that I had duplicate columns in several of the hundreds of dataframes I was trying to concat, each with dozens of enigmatic varnames. Manually searching for duplicates was not practical.

In case anyone else has the same problem, I wrote the following function which might help out.

def duplicated_varnames(df):
"""Return a dict of all variable names that
are duplicated in a given dataframe."""
repeat_dict = {}
var_list = list(df) # list of varnames as strings
for varname in var_list:
# make a list of all instances of that varname
test_list = [v for v in var_list if v == varname]
# if more than one instance, report duplications in repeat_dict
if len(test_list) > 1:
repeat_dict[varname] = len(test_list)
return repeat_dict

Then you can iterate over that dict to report how many duplicates there are, delete the duplicated variables, or rename them in some systematic way.

Wrote a small function to concatenate duplicated column names. Function cares about sorting if original dataframe is unsorted, the output will be a sorted one.

def concat_duplicate_columns(df):
dupli = {}
# populate dictionary with column names and count for duplicates
for column in df.columns:
dupli[column] = dupli[column] + 1 if column in dupli.keys() else 1
# rename duplicated keys with °°° number suffix
for key, val in dict(dupli).items():
del dupli[key]
if val > 1:
for i in range(val):
dupli[key+'°°°'+str(i)] = val
else: dupli[key] = 1
# rename columns so that we can now access abmigous column names
# sorting in dict is the same as in original table
df.columns = dupli.keys()
# for each duplicated column name
for i in set(re.sub('°°°(.*)','',j) for j in dupli.keys() if '°°°' in j):
i = str(i)
# for each duplicate of a column name
for k in range(dupli[i+'°°°0']-1):
# concatenate values in duplicated columns
df[i+'°°°0'] = df[i+'°°°0'].astype(str) + df[i+'°°°'+str(k+1)].astype(str)
# Drop duplicated columns from which we have aquired data
df = df.drop(i+'°°°'+str(k+1), 1)
# resort column names for proper mapping
df = df.reindex_axis(sorted(df.columns), axis = 1)
# rename columns
df.columns = sorted(set(re.sub('°°°(.*)','',i) for i in dupli.keys()))
return df

You need to have the same header names for all the df you want to concat.

Do it for example with :

headername = list(df)

Data = Data.filter(headername)

How to reproduce above error from pandas.concat(...):

ValueError: Plan shapes are not aligned

The Python (3.6.8) code:

import pandas as pd
df = pd.DataFrame({"foo": [3] })
print(df)
df2 = pd.concat([df, df], axis="columns")
print(df2)
df3 = pd.concat([df2, df], sort=False) #ValueError: Plan shapes are not aligned

which prints:

   foo
0    3


foo  foo
0    3    3
ValueError: Plan shapes are not aligned

Explanation of error

If the first pandas dataframe (here df2) has a duplicate named column and is sent to pd.concat and the second dataframe isn't of the same dimension as the first, then you get this error.

Solution

Make sure there are no duplicate named columns:

df_onefoo = pd.DataFrame({"foo": [3] })
print(df_onefoo)
df_onebar = pd.DataFrame({"bar": [3] })
print(df_onebar)
df2 = pd.concat([df_onefoo, df_onebar], axis="columns")
print(df2)
df3 = pd.concat([df2, df_onefoo], sort=False)
print(df2)

prints:

   foo
0    3


bar
0    3


foo  bar
0    3    3


foo  bar
0    3    3

Pandas concat could have been more helpful with that error message. It's a straight up bubbleup-implementation-itis, which is textbook python.

错误是由于有重复的列。使用以下功能，以便在不影响数据的情况下删除重复的功能。

def duplicated_varnames(df):
repeat_dict = {}
var_list = list(df) # list of varnames as strings
for varname in var_list:
test_list = [v for v in var_list if v == varname]
if len(test_list) > 1:
repeat_dict[varname] = len(test_list)
if len(repeat_dict)>0:
df = df.loc[:,~df.columns.duplicated()]
return df

I was receiving the ValueError: Plan shapes are not aligned when adding dataframes together. I was trying to loop over Excel sheets and after cleaning concacting them together.

The error was being raised as their were multiple none columns which I dropped with the code below:

df = df.loc[:, df.columns.notnull()] # found on stackoverflow