Sorting for pandas category dtype

[gothmania]

I'm creating table one for some ordered panda category columns (pandas.Categorical). Can you provide an option to sort the results in the order of levels, not in the alphabet order? It would be best if we could sort both the result rows and (groupby) columns.

For example: levels disagree < neutral < agree

At the moment:

                     overall
variable  level
some_var  agree      XX (XX)
          disagree   XX (XX)
          neutral    XX (XX)

It should be:

                     overall
variable  level
some_var  disagree   XX (XX)
          neutral    XX (XX)
          agree      XX (XX)

Or when grouped:

                   disagree    neutral    agree
variable level
some_var           XX (XX)     XX (XX)    XX (XX)

It's just the matter of appearance, but I think the table will be more ready to publish. At the moment I have to rearrange the rows and columns manually.

Thanks.

[tompollard]

Thanks, we'll look into adding this sorting functionality when we have the opportunity.

[tompollard]

It is now (from v0.6.6) possible to specify custom ordering for categorical variables using the order argument. Example below:

# import libraries
from tableone import TableOne
import pandas as pd

# load sample data into a pandas dataframe
url="https://raw.githubusercontent.com/tompollard/tableone/master/data/pn2012_demo.csv"
data=pd.read_csv(url)

# columns to summarize
columns = ['SysABP', 'ICU', 'Height', 'Weight']

# columns containing categorical variables
categorical = ['ICU']

order = {'ICU': ['SICU', 'MICU', 'CSRU', 'CCU']}

# create tableone with the input arguments
mytable = TableOne(data, columns=columns, categorical=categorical, 
                   label_suffix=True, groupby = 'death', order=order)

print(mytable.tabulate(tablefmt = "github"))

		Missing	0	1
n			864	136
SysABP, mean (SD)		291	115.4 (38.3)	107.6 (49.4)
ICU, n (%)	SICU	0	215 (24.9)	41 (30.1)
	MICU		318 (36.8)	62 (45.6)
	CSRU		194 (22.5)	8 (5.9)
	CCU		137 (15.9)	25 (18.4)
Height, mean (SD)		475	170.3 (23.2)	168.5 (11.3)
Weight, mean (SD)		302	83.0 (23.6)	82.3 (25.4)

[gothmania]

This is of extremely great help to me. Thank you so much, Tom.

[tompollard]

thanks @gothmania, glad it helps