Remove low frequency values from pandas.dataframe

I see there are two ways you might want to do this.

For the entire DataFrame

This method removes the values that occur infrequently in the entire DataFrame. We can do it without loops, using built-in functions to speed things up.

import pandas as pd
import numpy as np

df = pd.DataFrame(np.random.randint(0, high=9, size=(100,2)),
         columns = ['A', 'B'])

threshold = 10 # Anything that occurs less than this will be removed.
value_counts = df.stack().value_counts() # Entire DataFrame 
to_remove = value_counts[value_counts <= threshold].index
df.replace(to_remove, np.nan, inplace=True)

Column-by-column

This method removes the entries that occur infrequently in each column.

import pandas as pd
import numpy as np

df = pd.DataFrame(np.random.randint(0, high=9, size=(100,2)),
         columns = ['A', 'B'])

threshold = 10 # Anything that occurs less than this will be removed.
for col in df.columns:
    value_counts = df[col].value_counts() # Specific column 
    to_remove = value_counts[value_counts <= threshold].index
    df[col].replace(to_remove, np.nan, inplace=True)

You probably don't want to remove the entire row in your DataFrame if only one column has values below your threshold, so I've simply removed these data points and replaced them with None.

I loop through each column and perform a value_counts on each. I then get the index values for each items that occurs at or below the target threshold values. Finally, I use .loc to locate these elements values in the column and then replace them with None.

df = pd.DataFrame({'A': ['a', 'b', 'b', 'c', 'c'], 
                   'B': ['a', 'a', 'b', 'c', 'c'], 
                   'C': ['a', 'a', 'b', 'b', 'c']})

>>> df
   A  B  C
0  a  a  a
1  b  a  a
2  b  b  b
3  c  c  b
4  c  c  c

threshold = 1  # Remove items less than or equal to threshold
for col in df:
    vc = df[col].value_counts()
    vals_to_remove = vc[vc <= threshold].index.values
    df[col].loc[df[col].isin(vals_to_remove)] = None

>>> df
      A     B     C
0  None     a     a
1     b     a     a
2     b  None     b
3     c     c     b
4     c     c  None