Python – Making heatmap from pandas DataFrame

dataframeheatmappandaspython

I have a dataframe generated from Python's Pandas package. How can I generate heatmap using DataFrame from pandas package.

import numpy as np 
from pandas import *

Index= ['aaa','bbb','ccc','ddd','eee']
Cols = ['A', 'B', 'C','D']
df = DataFrame(abs(np.random.randn(5, 4)), index= Index, columns=Cols)

>>> df
          A         B         C         D
aaa  2.431645  1.248688  0.267648  0.613826
bbb  0.809296  1.671020  1.564420  0.347662
ccc  1.501939  1.126518  0.702019  1.596048
ddd  0.137160  0.147368  1.504663  0.202822
eee  0.134540  3.708104  0.309097  1.641090
>>>

Best Answer

For people looking at this today, I would recommend the Seaborn heatmap() as documented here.

The example above would be done as follows:

import numpy as np 
from pandas import DataFrame
import seaborn as sns
%matplotlib inline

Index= ['aaa', 'bbb', 'ccc', 'ddd', 'eee']
Cols = ['A', 'B', 'C', 'D']
df = DataFrame(abs(np.random.randn(5, 4)), index=Index, columns=Cols)

sns.heatmap(df, annot=True)

Where %matplotlib is an IPython magic function for those unfamiliar.

Related Solutions

Python – Selecting multiple columns in a Pandas dataframe

The column names (which are strings) cannot be sliced in the manner you tried.

Here you have a couple of options. If you know from context which variables you want to slice out, you can just return a view of only those columns by passing a list into the __getitem__ syntax (the []'s).

df1 = df[['a', 'b']]

Alternatively, if it matters to index them numerically and not by their name (say your code should automatically do this without knowing the names of the first two columns) then you can do this instead:

df1 = df.iloc[:, 0:2] # Remember that Python does not slice inclusive of the ending index.

Additionally, you should familiarize yourself with the idea of a view into a Pandas object vs. a copy of that object. The first of the above methods will return a new copy in memory of the desired sub-object (the desired slices).

Sometimes, however, there are indexing conventions in Pandas that don't do this and instead give you a new variable that just refers to the same chunk of memory as the sub-object or slice in the original object. This will happen with the second way of indexing, so you can modify it with the .copy() method to get a regular copy. When this happens, changing what you think is the sliced object can sometimes alter the original object. Always good to be on the look out for this.

df1 = df.iloc[0, 0:2].copy() # To avoid the case where changing df1 also changes df

To use iloc, you need to know the column positions (or indices). As the column positions may change, instead of hard-coding indices, you can use iloc along with get_loc function of columns method of dataframe object to obtain column indices.

{df.columns.get_loc(c): c for idx, c in enumerate(df.columns)}

Now you can use this dictionary to access columns through names and using iloc.

Python – Renaming column names in Pandas

RENAME SPECIFIC COLUMNS

Use the df.rename() function and refer the columns to be renamed. Not all the columns have to be renamed:

df = df.rename(columns={'oldName1': 'newName1', 'oldName2': 'newName2'})
# Or rename the existing DataFrame (rather than creating a copy) 
df.rename(columns={'oldName1': 'newName1', 'oldName2': 'newName2'}, inplace=True)

Minimal Code Example

df = pd.DataFrame('x', index=range(3), columns=list('abcde'))
df

   a  b  c  d  e
0  x  x  x  x  x
1  x  x  x  x  x
2  x  x  x  x  x

The following methods all work and produce the same output:

df2 = df.rename({'a': 'X', 'b': 'Y'}, axis=1)  # new method
df2 = df.rename({'a': 'X', 'b': 'Y'}, axis='columns')
df2 = df.rename(columns={'a': 'X', 'b': 'Y'})  # old method  

df2

   X  Y  c  d  e
0  x  x  x  x  x
1  x  x  x  x  x
2  x  x  x  x  x

Remember to assign the result back, as the modification is not-inplace. Alternatively, specify inplace=True:

df.rename({'a': 'X', 'b': 'Y'}, axis=1, inplace=True)
df

   X  Y  c  d  e
0  x  x  x  x  x
1  x  x  x  x  x
2  x  x  x  x  x

From v0.25, you can also specify errors='raise' to raise errors if an invalid column-to-rename is specified. See v0.25 rename() docs.

REASSIGN COLUMN HEADERS

Use df.set_axis() with axis=1 and inplace=False (to return a copy).

df2 = df.set_axis(['V', 'W', 'X', 'Y', 'Z'], axis=1, inplace=False)
df2

   V  W  X  Y  Z
0  x  x  x  x  x
1  x  x  x  x  x
2  x  x  x  x  x

This returns a copy, but you can modify the DataFrame in-place by setting inplace=True (this is the default behaviour for versions <=0.24 but is likely to change in the future).

You can also assign headers directly:

df.columns = ['V', 'W', 'X', 'Y', 'Z']
df

   V  W  X  Y  Z
0  x  x  x  x  x
1  x  x  x  x  x
2  x  x  x  x  x