The icikt Tutorial

Importing icikt package

If the icikt package is installed, it can be imported:

import icikt

Using icikt in the command-line interface

The iciktArray function can be accessed from the command line interface:

Either the "icikt" command or "python3 -m icikt" can be used to run the command line interface.

> icikt -h

Usage:
    icikt.py iciktArray <dataFilePath> [--data-format=<format>] [--replace=<globalNA>] [--mode=<perspective>] [--scale=<scaleMax>] [--diag=<diagGood>] [--chunk=<chunkSize>] [--output=<outname>] [--include=<includeOnly>]
    icikt.py leftCensor <dataFilePath> [--data-format=<format>] [--replace=<globalNA>] [--samples=<sampleClasses>]
    icikt.py -h | --help
    icikt.py --version

Using a csv file with no global replace values:

icikt iciktArray /path/to/file.csv --data-format=csv --replace=None

Using a tsv file with no replacements and outputting the results with prefix of ‘test’:

icikt iciktArray /path/to/file.tsv --data-format=tsv --replace= --output=test

Using a csv file in local mode with 0 as the replace value, no scaling, no diagonal values, and a chunk size of 5:

icikt iciktArray /path/to/file.csv --replace=0 --mode=local --scale=False --diag=False --chunk=5

Using icikt in a Python script

Import numpy and icikt:

import numpy as np
import icikt

Generate a numpy array from your data file:

dataArray = np.genfromtxt('path/to/file.tsv', delimiter='\t')

Call iciktArray on your dataArray, saving outputs to separate variables:

out, corr, pVal, tMax = icikt.iciktArray(dataArray)
print(out,corr,pVal,tMax,sep='\n\n')

# saving outputs to files
np.savetxt('outArray.csv', out, delimiter=',')
np.savetxt('corrArray.csv', corr, delimiter=',')
np.savetxt('pValArray.csv', pVal, delimiter=',')
np.savetxt('tMaxArray.csv', tMax, delimiter=',')