How to pivot a dataframe?

python pandas group-by pivot pandas-groupby
piRSquared picture piRSquared · Nov 7, 2017 · Viewed 33k times · Source
  • What is pivot?
  • How do I pivot?
  • Is this a pivot?
  • Long format to wide format?

I've seen a lot of questions that ask about pivot tables. Even if they don't know that they are asking about pivot tables, they usually are. It is virtually impossible to write a canonical question and answer that encompasses all aspects of pivoting...

... But I'm going to give it a go.

The problem with existing questions and answers is that often the question is focused on a nuance that the OP has trouble generalizing in order to use a number of the existing good answers. However, none of the answers attempt to give a comprehensive explanation (because it's a daunting task)

Look a few examples from my google search

  1. How to pivot a dataframe in Pandas?
  • Good question and answer. But the answer only answers the specific question with little explanation.
  1. pandas pivot table to data frame
  • In this question, the OP is concerned with the output of the pivot. Namely how the columns look. OP wanted it to look like R. This isn't very helpful for pandas users.
  1. pandas pivoting a dataframe, duplicate rows
  • Another decent question but the answer focuses on one method, namely pd.DataFrame.pivot

So whenever someone searches for pivot they get sporadic results that are likely not going to answer their specific question.

Setup

You may notice that I conspicuously named my columns and relevant column values to correspond with how I'm going to pivot in the answers below.

import numpy as np
import pandas as pd
from numpy.core.defchararray import add

np.random.seed([3,1415])
n = 20

cols = np.array(['key', 'row', 'item', 'col'])
arr1 = (np.random.randint(5, size=(n, 4)) // [2, 1, 2, 1]).astype(str)

df = pd.DataFrame(
    add(cols, arr1), columns=cols
).join(
    pd.DataFrame(np.random.rand(n, 2).round(2)).add_prefix('val')
)
print(df)

     key   row   item   col  val0  val1
0   key0  row3  item1  col3  0.81  0.04
1   key1  row2  item1  col2  0.44  0.07
2   key1  row0  item1  col0  0.77  0.01
3   key0  row4  item0  col2  0.15  0.59
4   key1  row0  item2  col1  0.81  0.64
5   key1  row2  item2  col4  0.13  0.88
6   key2  row4  item1  col3  0.88  0.39
7   key1  row4  item1  col1  0.10  0.07
8   key1  row0  item2  col4  0.65  0.02
9   key1  row2  item0  col2  0.35  0.61
10  key2  row0  item2  col1  0.40  0.85
11  key2  row4  item1  col2  0.64  0.25
12  key0  row2  item2  col3  0.50  0.44
13  key0  row4  item1  col4  0.24  0.46
14  key1  row3  item2  col3  0.28  0.11
15  key0  row3  item1  col1  0.31  0.23
16  key0  row0  item2  col3  0.86  0.01
17  key0  row4  item0  col3  0.64  0.21
18  key2  row2  item2  col0  0.13  0.45
19  key0  row2  item0  col4  0.37  0.70

Question(s)

  1. Why do I get ValueError: Index contains duplicate entries, cannot reshape

  2. How do I pivot df such that the col values are columns, row values are the index, and mean of val0 are the values?

     col   col0   col1   col2   col3  col4
 row                                  
 row0  0.77  0.605    NaN  0.860  0.65
 row2  0.13    NaN  0.395  0.500  0.25
 row3   NaN  0.310    NaN  0.545   NaN
 row4   NaN  0.100  0.395  0.760  0.24

  3. How do I pivot df such that the col values are columns, row values are the index, mean of val0 are the values, and missing values are 0?

     col   col0   col1   col2   col3  col4
 row                                  
 row0  0.77  0.605  0.000  0.860  0.65
 row2  0.13  0.000  0.395  0.500  0.25
 row3  0.00  0.310  0.000  0.545  0.00
 row4  0.00  0.100  0.395  0.760  0.24

  4. Can I get something other than mean, like maybe sum?

     col   col0  col1  col2  col3  col4
 row                               
 row0  0.77  1.21  0.00  0.86  0.65
 row2  0.13  0.00  0.79  0.50  0.50
 row3  0.00  0.31  0.00  1.09  0.00
 row4  0.00  0.10  0.79  1.52  0.24

  5. Can I do more that one aggregation at a time?

            sum                          mean                           
 col   col0  col1  col2  col3  col4  col0   col1   col2   col3  col4
 row                                                                
 row0  0.77  1.21  0.00  0.86  0.65  0.77  0.605  0.000  0.860  0.65
 row2  0.13  0.00  0.79  0.50  0.50  0.13  0.000  0.395  0.500  0.25
 row3  0.00  0.31  0.00  1.09  0.00  0.00  0.310  0.000  0.545  0.00
 row4  0.00  0.10  0.79  1.52  0.24  0.00  0.100  0.395  0.760  0.24

  6. Can I aggregate over multiple value columns?

           val0                             val1                          
 col   col0   col1   col2   col3  col4  col0   col1  col2   col3  col4
 row                                                                  
 row0  0.77  0.605  0.000  0.860  0.65  0.01  0.745  0.00  0.010  0.02
 row2  0.13  0.000  0.395  0.500  0.25  0.45  0.000  0.34  0.440  0.79
 row3  0.00  0.310  0.000  0.545  0.00  0.00  0.230  0.00  0.075  0.00
 row4  0.00  0.100  0.395  0.760  0.24  0.00  0.070  0.42  0.300  0.46

  7. Can Subdivide by multiple columns?

     item item0             item1                         item2                   
 col   col2  col3  col4  col0  col1  col2  col3  col4  col0   col1  col3  col4
 row                                                                          
 row0  0.00  0.00  0.00  0.77  0.00  0.00  0.00  0.00  0.00  0.605  0.86  0.65
 row2  0.35  0.00  0.37  0.00  0.00  0.44  0.00  0.00  0.13  0.000  0.50  0.13
 row3  0.00  0.00  0.00  0.00  0.31  0.00  0.81  0.00  0.00  0.000  0.28  0.00
 row4  0.15  0.64  0.00  0.00  0.10  0.64  0.88  0.24  0.00  0.000  0.00  0.00

  8. Or

     item      item0             item1                         item2                  
 col        col2  col3  col4  col0  col1  col2  col3  col4  col0  col1  col3  col4
 key  row                                                                         
 key0 row0  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.86  0.00
      row2  0.00  0.00  0.37  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.50  0.00
      row3  0.00  0.00  0.00  0.00  0.31  0.00  0.81  0.00  0.00  0.00  0.00  0.00
      row4  0.15  0.64  0.00  0.00  0.00  0.00  0.00  0.24  0.00  0.00  0.00  0.00
 key1 row0  0.00  0.00  0.00  0.77  0.00  0.00  0.00  0.00  0.00  0.81  0.00  0.65
      row2  0.35  0.00  0.00  0.00  0.00  0.44  0.00  0.00  0.00  0.00  0.00  0.13
      row3  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.28  0.00
      row4  0.00  0.00  0.00  0.00  0.10  0.00  0.00  0.00  0.00  0.00  0.00  0.00
 key2 row0  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.40  0.00  0.00
      row2  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.13  0.00  0.00  0.00
      row4  0.00  0.00  0.00  0.00  0.00  0.64  0.88  0.00  0.00  0.00  0.00  0.00

  9. Can I aggregate the frequency in which the column and rows occur together, aka "cross tabulation"?

     col   col0  col1  col2  col3  col4
 row                               
 row0     1     2     0     1     1
 row2     1     0     2     1     2
 row3     0     1     0     2     0
 row4     0     1     2     2     1

  10. How do I convert a DataFrame from long to wide by pivoting on ONLY two columns? Given,

    np.random.seed([3, 1415])
df2 = pd.DataFrame({'A': list('aaaabbbc'), 'B': np.random.choice(15, 8)})        
df2        
   A   B
0  a   0
1  a  11
2  a   2
3  a  11
4  b  10
5  b  10
6  b  14
7  c   7

    The expected should look something like

          a     b    c
0   0.0  10.0  7.0
1  11.0  10.0  NaN
2   2.0  14.0  NaN
3  11.0   NaN  NaN

  11. How do I flatten the multiple index to single index after pivot

    From

       1  2   
   1  1  2        
a  2  1  1
b  2  1  0
c  1  0  0

    To

       1|1  2|1  2|2               
a    2    1    1
b    2    1    0
c    1    0    0

Answer

piRSquared picture piRSquared · Nov 7, 2017

We start by answering the first question:

Question 1

Why do I get ValueError: Index contains duplicate entries, cannot reshape

This occurs because pandas is attempting to reindex either a columns or index object with duplicate entries. There are varying methods to use that can perform a pivot. Some of them are not well suited to when there are duplicates of the keys in which it is being asked to pivot on. For example. Consider pd.DataFrame.pivot. I know there are duplicate entries that share the row and col values:

df.duplicated(['row', 'col']).any()

True

So when I pivot using

df.pivot(index='row', columns='col', values='val0')

I get the error mentioned above. In fact, I get the same error when I try to perform the same task with:

df.set_index(['row', 'col'])['val0'].unstack()

Here is a list of idioms we can use to pivot

  1. pd.DataFrame.groupby + pd.DataFrame.unstack
    • Good general approach for doing just about any type of pivot
    • You specify all columns that will constitute the pivoted row levels and column levels in one group by. You follow that by selecting the remaining columns you want to aggregate and the function(s) you want to perform the aggregation. Finally, you unstack the levels that you want to be in the column index.
  2. pd.DataFrame.pivot_table
    • A glorified version of groupby with more intuitive API. For many people, this is the preferred approach. And is the intended approach by the developers.
    • Specify row level, column levels, values to be aggregated, and function(s) to perform aggregations.
  3. pd.DataFrame.set_index + pd.DataFrame.unstack
    • Convenient and intuitive for some (myself included). Cannot handle duplicate grouped keys.
    • Similar to the groupby paradigm, we specify all columns that will eventually be either row or column levels and set those to be the index. We then unstack the levels we want in the columns. If either the remaining index levels or column levels are not unique, this method will fail.
  4. pd.DataFrame.pivot
    • Very similar to set_index in that it shares the duplicate key limitation. The API is very limited as well. It only takes scalar values for index, columns, values.
    • Similar to the pivot_table method in that we select rows, columns, and values on which to pivot. However, we cannot aggregate and if either rows or columns are not unique, this method will fail.
  5. pd.crosstab
    • This a specialized version of pivot_table and in it's purest form is the most intuitive way to perform several tasks.
  6. pd.factorize + np.bincount
    • This is a highly advanced technique that is very obscure but is very fast. It cannot be used in all circumstances, but when it can be used and you are comfortable using it, you will reap the performance rewards.
  7. pd.get_dummies + pd.DataFrame.dot
    • I use this for cleverly performing cross tabulation.

Examples

What I'm going to do for each subsequent answer and question is to answer it using pd.DataFrame.pivot_table. Then I'll provide alternatives to perform the same task.

Question 3

How do I pivot df such that the col values are columns, row values are the index, mean of val0 are the values, and missing values are 0?

  • pd.DataFrame.pivot_table

    • fill_value is not set by default. I tend to set it appropriately. In this case I set it to 0. Notice I skipped question 2 as it's the same as this answer without the fill_value

    • aggfunc='mean' is the default and I didn't have to set it. I included it to be explicit.

      df.pivot_table(
    values='val0', index='row', columns='col',
    fill_value=0, aggfunc='mean')

col   col0   col1   col2   col3  col4
row                                  
row0  0.77  0.605  0.000  0.860  0.65
row2  0.13  0.000  0.395  0.500  0.25
row3  0.00  0.310  0.000  0.545  0.00
row4  0.00  0.100  0.395  0.760  0.24

  • pd.DataFrame.groupby

    df.groupby(['row', 'col'])['val0'].mean().unstack(fill_value=0)

  • pd.crosstab

    pd.crosstab(
    index=df['row'], columns=df['col'],
    values=df['val0'], aggfunc='mean').fillna(0)

Question 4

Can I get something other than mean, like maybe sum?

  • pd.DataFrame.pivot_table

    df.pivot_table(
    values='val0', index='row', columns='col',
    fill_value=0, aggfunc='sum')

col   col0  col1  col2  col3  col4
row                               
row0  0.77  1.21  0.00  0.86  0.65
row2  0.13  0.00  0.79  0.50  0.50
row3  0.00  0.31  0.00  1.09  0.00
row4  0.00  0.10  0.79  1.52  0.24

  • pd.DataFrame.groupby

    df.groupby(['row', 'col'])['val0'].sum().unstack(fill_value=0)

  • pd.crosstab

    pd.crosstab(
    index=df['row'], columns=df['col'],
    values=df['val0'], aggfunc='sum').fillna(0)

Question 5

Can I do more that one aggregation at a time?

Notice that for pivot_table and crosstab I needed to pass list of callables. On the other hand, groupby.agg is able to take strings for a limited number of special functions. groupby.agg would also have taken the same callables we passed to the others, but it is often more efficient to leverage the string function names as there are efficiencies to be gained.

  • pd.DataFrame.pivot_table

    df.pivot_table(
    values='val0', index='row', columns='col',
    fill_value=0, aggfunc=[np.size, np.mean])

     size                      mean                           
col  col0 col1 col2 col3 col4  col0   col1   col2   col3  col4
row                                                           
row0    1    2    0    1    1  0.77  0.605  0.000  0.860  0.65
row2    1    0    2    1    2  0.13  0.000  0.395  0.500  0.25
row3    0    1    0    2    0  0.00  0.310  0.000  0.545  0.00
row4    0    1    2    2    1  0.00  0.100  0.395  0.760  0.24

  • pd.DataFrame.groupby

    df.groupby(['row', 'col'])['val0'].agg(['size', 'mean']).unstack(fill_value=0)

  • pd.crosstab

    pd.crosstab(
    index=df['row'], columns=df['col'],
    values=df['val0'], aggfunc=[np.size, np.mean]).fillna(0, downcast='infer')

Question 6

Can I aggregate over multiple value columns?

  • pd.DataFrame.pivot_table we pass values=['val0', 'val1'] but we could've left that off completely

    df.pivot_table(
    values=['val0', 'val1'], index='row', columns='col',
    fill_value=0, aggfunc='mean')

      val0                             val1                          
col   col0   col1   col2   col3  col4  col0   col1  col2   col3  col4
row                                                                  
row0  0.77  0.605  0.000  0.860  0.65  0.01  0.745  0.00  0.010  0.02
row2  0.13  0.000  0.395  0.500  0.25  0.45  0.000  0.34  0.440  0.79
row3  0.00  0.310  0.000  0.545  0.00  0.00  0.230  0.00  0.075  0.00
row4  0.00  0.100  0.395  0.760  0.24  0.00  0.070  0.42  0.300  0.46

  • pd.DataFrame.groupby

    df.groupby(['row', 'col'])['val0', 'val1'].mean().unstack(fill_value=0)

Question 7

Can Subdivide by multiple columns?

  • pd.DataFrame.pivot_table

    df.pivot_table(
    values='val0', index='row', columns=['item', 'col'],
    fill_value=0, aggfunc='mean')

item item0             item1                         item2                   
col   col2  col3  col4  col0  col1  col2  col3  col4  col0   col1  col3  col4
row                                                                          
row0  0.00  0.00  0.00  0.77  0.00  0.00  0.00  0.00  0.00  0.605  0.86  0.65
row2  0.35  0.00  0.37  0.00  0.00  0.44  0.00  0.00  0.13  0.000  0.50  0.13
row3  0.00  0.00  0.00  0.00  0.31  0.00  0.81  0.00  0.00  0.000  0.28  0.00
row4  0.15  0.64  0.00  0.00  0.10  0.64  0.88  0.24  0.00  0.000  0.00  0.00

  • pd.DataFrame.groupby

    df.groupby(
    ['row', 'item', 'col']
)['val0'].mean().unstack(['item', 'col']).fillna(0).sort_index(1)

Question 8

Can Subdivide by multiple columns?

  • pd.DataFrame.pivot_table

    df.pivot_table(
    values='val0', index=['key', 'row'], columns=['item', 'col'],
    fill_value=0, aggfunc='mean')

item      item0             item1                         item2                  
col        col2  col3  col4  col0  col1  col2  col3  col4  col0  col1  col3  col4
key  row                                                                         
key0 row0  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.86  0.00
     row2  0.00  0.00  0.37  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.50  0.00
     row3  0.00  0.00  0.00  0.00  0.31  0.00  0.81  0.00  0.00  0.00  0.00  0.00
     row4  0.15  0.64  0.00  0.00  0.00  0.00  0.00  0.24  0.00  0.00  0.00  0.00
key1 row0  0.00  0.00  0.00  0.77  0.00  0.00  0.00  0.00  0.00  0.81  0.00  0.65
     row2  0.35  0.00  0.00  0.00  0.00  0.44  0.00  0.00  0.00  0.00  0.00  0.13
     row3  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.28  0.00
     row4  0.00  0.00  0.00  0.00  0.10  0.00  0.00  0.00  0.00  0.00  0.00  0.00
key2 row0  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.40  0.00  0.00
     row2  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.13  0.00  0.00  0.00
     row4  0.00  0.00  0.00  0.00  0.00  0.64  0.88  0.00  0.00  0.00  0.00  0.00

  • pd.DataFrame.groupby

    df.groupby(
    ['key', 'row', 'item', 'col']
)['val0'].mean().unstack(['item', 'col']).fillna(0).sort_index(1)

  • pd.DataFrame.set_index because the set of keys are unique for both rows and columns

    df.set_index(
    ['key', 'row', 'item', 'col']
)['val0'].unstack(['item', 'col']).fillna(0).sort_index(1)

Question 9

Can I aggregate the frequency in which the column and rows occur together, aka "cross tabulation"?

  • pd.DataFrame.pivot_table

    df.pivot_table(index='row', columns='col', fill_value=0, aggfunc='size')

    col   col0  col1  col2  col3  col4
row                               
row0     1     2     0     1     1
row2     1     0     2     1     2
row3     0     1     0     2     0
row4     0     1     2     2     1

  • pd.DataFrame.groupby

    df.groupby(['row', 'col'])['val0'].size().unstack(fill_value=0)

  • pd.crosstab

    pd.crosstab(df['row'], df['col'])

  • pd.factorize + np.bincount

    # get integer factorization `i` and unique values `r`
# for column `'row'`
i, r = pd.factorize(df['row'].values)
# get integer factorization `j` and unique values `c`
# for column `'col'`
j, c = pd.factorize(df['col'].values)
# `n` will be the number of rows
# `m` will be the number of columns
n, m = r.size, c.size
# `i * m + j` is a clever way of counting the 
# factorization bins assuming a flat array of length
# `n * m`.  Which is why we subsequently reshape as `(n, m)`
b = np.bincount(i * m + j, minlength=n * m).reshape(n, m)
# BTW, whenever I read this, I think 'Bean, Rice, and Cheese'
pd.DataFrame(b, r, c)

      col3  col2  col0  col1  col4
row3     2     0     0     1     0
row2     1     2     1     0     2
row0     1     0     1     2     1
row4     2     2     0     1     1

  • pd.get_dummies

    pd.get_dummies(df['row']).T.dot(pd.get_dummies(df['col']))

      col0  col1  col2  col3  col4
row0     1     2     0     1     1
row2     1     0     2     1     2
row3     0     1     0     2     0
row4     0     1     2     2     1

Question 10

How do I convert a DataFrame from long to wide by pivoting on ONLY two columns?

The first step is to assign a number to each row - this number will be the row index of that value in the pivoted result. This is done using GroupBy.cumcount:

df2.insert(0, 'count', df.groupby('A').cumcount())
df2

   count  A   B
0      0  a   0
1      1  a  11
2      2  a   2
3      3  a  11
4      0  b  10
5      1  b  10
6      2  b  14
7      0  c   7

The second step is to use the newly created column as the index to call DataFrame.pivot. 

df2.pivot(*df)
# df.pivot(index='count', columns='A', values='B')

A         a     b    c
count                 
0       0.0  10.0  7.0
1      11.0  10.0  NaN
2       2.0  14.0  NaN
3      11.0   NaN  NaN

Question 11

How do I flatten the multiple index to single index after pivot

If columns type object with string join 

df.columns = df.columns.map('|'.join)

else format

df.columns = df.columns.map('{0[0]}|{0[1]}'.format)

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I am using this data frame: Fruit Date Name Number Apples 10/6/2016 Bob 7 Apples 10/6/2016 Bob 8 Apples 10/6/2016 Mike 9 Apples 10/7/2016 Steve 10 Apples 10/7/2016 Bob 1 Oranges 10/7/2016 Bob 2 Oranges 10/6/2016 Tom 15 Oranges 10/6/2016 Mike 57 Oranges 10/6/2016 Bob 65 Oranges 10/7/2016 Tony 1 Grapes 10/7/2016 Bob 1 Grapes 10/7/2016 Tom 87 Grapes 10/7/2016 Bob 22 Grapes 10/7/2016 Bob 12 Grapes 10/7/2016 Tony 15 …

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