Python Pandas - Pivot table aggregating wrong column [duplicate]

Question

How do I pivot the pandas dataframe below such that the col values become columns, row values become the index, and mean of val0 becomes the values? (In some cases this is called transforming from long-format to wide-format.)

Consider a dataframe df with columns 'key', 'row', 'item', 'col', and random float values 'val0', 'val1'. I conspicuously named the columns and relevant column values to correspond with how I want to pivot them. (Setup code at bottom.)

     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

Subquestions

How to avoid getting ValueError: Index contains duplicate entries, cannot reshape?

How do I pivot df such that the col values become columns, row values become 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

How do I pivot...

... so that 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

... to do an aggregate function other than mean, like 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

... to 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

... to 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

... to subdivide by multiple columns? (item0,item1,item2..., col0,col1,col2...)

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

... to subdivide by multiple rows: (key0,key1... row0,row1,row2...)

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

... to 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

... to 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

How do I flatten the multi-index to single index after pivot?

From:

To:

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

Setup

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)

Why is this question not a duplicate? and more useful than the following autosuggestions:

How to pivot a dataframe in Pandas? only covers the specific case of 'Country' to row-index, values of 'Indicator' for 'Year' to multiple columns and no aggregation of values.
When pivoting a Pandas dataframe, how do I make the column names the same as in R? (flat, label in column names) asks how to pivot in pandas like in R, i.e. autogenerate an individual column for each value of strength...
pandas pivoting a dataframe, duplicate rows asks about the syntax for pivoting multiple columns, without needing to list them all.

None of the existing questions and answers are comprehensive, so this is an attempt at a canonical question and answer that encompasses all aspects of pivoting.

piRSquared · Accepted Answer

Here is a list of idioms we can use to pivot

pd.DataFrame.pivot_table
- A glorified version of groupby with more intuitive API. For many people, this is the preferred approach. And it is the intended approach by the developers.
- Specify row level, column levels, values to be aggregated, and function(s) to perform aggregations.
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.
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.
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.
pd.crosstab
- This a specialized version of pivot_table and in its purest form is the most intuitive way to perform several tasks.
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.
pd.get_dummies + pd.DataFrame.dot
- I use this for cleverly performing cross tabulation.

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 on which it is being asked to pivot. 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()

Examples

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

Questions 2 and 3

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

pd.DataFrame.pivot_table

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

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

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

How do I make it so that 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.

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 I 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 I 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?

DataFrame.pivot

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', df2.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(*df2)
# df2.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

DataFrame.pivot_table

Whereas DataFrame.pivot only accepts columns, DataFrame.pivot_table also accepts arrays, so the GroupBy.cumcount can be passed directly as the index without creating an explicit column.
```
df2.pivot_table(index=df2.groupby('A').cumcount(), columns='A', values='B')

A         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
```

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)

Ch3steR · Answer

To extend @piRSquared's answer another version of Question 10

Question 10.1

DataFrame:

d = data = {'A': {0: 1, 1: 1, 2: 1, 3: 2, 4: 2, 5: 3, 6: 5},
 'B': {0: 'a', 1: 'b', 2: 'c', 3: 'a', 4: 'b', 5: 'a', 6: 'c'}}
df = pd.DataFrame(d)

   A  B
0  1  a
1  1  b
2  1  c
3  2  a
4  2  b
5  3  a
6  5  c

Output:

   0     1     2
A
1  a     b     c
2  a     b  None
3  a  None  None
5  c  None  None

Using df.groupby and pd.Series.tolist

t = df.groupby('A')['B'].apply(list)
out = pd.DataFrame(t.tolist(),index=t.index)
out
   0     1     2
A
1  a     b     c
2  a     b  None
3  a  None  None
5  c  None  None

Or A much better alternative using pd.pivot_table with df.squeeze.

t = df.pivot_table(index='A',values='B',aggfunc=list).squeeze()
out = pd.DataFrame(t.tolist(),index=t.index)

Python Pandas - Pivot table aggregating wrong column [duplicate]

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Python Pandas - Pivot table aggregating wrong column [duplicate]

Tags:

python

pandas

group-by

pivot

pivot-table

Subquestions

Setup

piRSquared

2 Answers

Question 1

Examples

Questions 2 and 3

Question 4

Question 5

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Question 11

piRSquared

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