Welcome to icikt’s documentation!¶

icikt¶

Description¶

The icikt package handles missing data before calculating a correlation between datasets for variables. The missing values are treated as information from a left-centered distribution perspective and are included in the calculation of concordant and discordant pairs used in calculating the correlation value.

Full API documentation, user guide, and tutorial can be found on readthedocs

Installation¶

The icikt package runs under Python 3.4+. Use pip to install. Starting with Python 3.4, pip is included by default.

Install on Linux, Mac OS X¶

python3 -m pip install icikt

Install on Windows¶

py -3 -m pip install icikt

Upgrade on Linux, Mac OS X¶

python3 -m pip install icikt --upgrade

Upgrade on Windows¶

py -3 -m pip install icikt --upgrade

Get the source code¶

Code is available on GitHub: https://github.com/MoseleyBioinformaticsLab/icikt

To clone the repo, first make sure you have git installed:

git clone https://github.com/MoseleyBioinformaticsLab/icikt.git

Dependencies¶

The icikt package depends on several Python libraries:

docopt for a command line interface.
scipy and numpy for mathmatical calculations.
Cython for optimized performance.

NOTE- NumPy and Cython must be preinstalled in order for this package to work.

The pip command will install all dependencies automatically, but if you wish to install them manually, run the following commands:

docopt for a command line interface
To install the docopt Python library run the following:
python3 -m pip install docopt  # On Linux, Mac OS X
py -3 -m pip install docopt    # On Windows
scipy for performing the kendall-tau calculations
To install the scipy Python library run the following:
python3 -m pip install scipy  # On Linux, Mac OS X
py -3 -m pip install scipy    # On Windows
numpy for creating and modifying ndarrays of data
To install numpy run the following:
python3 -m pip install numpy  # On Linux, Mac OS X
py -3 -m pip install numpy    # On Windows
Cython for the cythonized kendall_dis method
To install the Cython Python library run the following:
python3 -m pip install Cython  # On Linux, Mac OS X
py -3 -m pip install Cython    # On Windows

WARNING- If the following pip error message is generated, then the python3 devel package must be installed:

"fatal error: Python.h: No such file or directory"

Basic usage¶

To use the icikt package, input a 2d array with n columns each representing an array of data for a variable. The iciktArray will return two n x n 2d arrays for correlations and p-values. Each element will correspond to the result of a combination of two columns in the input array. iciktArray can also be called from the command-line interface given the file path for the data along with several optional parameters(more in docs/tutorial).

Running through command line :

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

Running through python script :

import numpy as np
import icikt

dataArray = np.genfromtxt('/path/to/file.tsv', delimiter="\t")
# or with random values
dataArray = numpy.random.randn(100, 2)

# running just 2 arrays with icikt
corr, pVal, tMax = icikt.icikt(dataArray[:,0], dataArray[:,1])

# running all combinations with iciktArray
scaled, corrRaw, pVals, tauMax = icikt.iciktArray(dataArray)

License¶

A modified Clear BSD License

Redistribution and use in source and binary forms, with or without modification, are permitted (subject to the limitations in the disclaimer below) provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
If the source code is used in a published work, then proper citation of the source code must be included with the published work.

NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY’S PATENT RIGHTS ARE GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Documentation index:¶

icikt¶

Description¶

The icikt package handles missing data before calculating a correlation between datasets for variables. The missing values are treated as information from a left-centered distribution perspective and are included in the calculation of concordant and discordant pairs used in calculating the correlation value.

Full API documentation, user guide, and tutorial can be found on readthedocs

Installation¶

The icikt package runs under Python 3.4+. Use pip to install. Starting with Python 3.4, pip is included by default.

Install on Linux, Mac OS X¶

python3 -m pip install icikt

Install on Windows¶

py -3 -m pip install icikt

Upgrade on Linux, Mac OS X¶

python3 -m pip install icikt --upgrade

Upgrade on Windows¶

py -3 -m pip install icikt --upgrade

Get the source code¶

Code is available on GitHub: https://github.com/MoseleyBioinformaticsLab/icikt

To clone the repo, first make sure you have git installed:

git clone https://github.com/MoseleyBioinformaticsLab/icikt.git

Dependencies¶

The icikt package depends on several Python libraries:

docopt for a command line interface.
scipy and numpy for mathmatical calculations.
Cython for optimized performance.

NOTE- NumPy and Cython must be preinstalled in order for this package to work.

The pip command will install all dependencies automatically, but if you wish to install them manually, run the following commands:

docopt for a command line interface
To install the docopt Python library run the following:
python3 -m pip install docopt  # On Linux, Mac OS X
py -3 -m pip install docopt    # On Windows
scipy for performing the kendall-tau calculations
To install the scipy Python library run the following:
python3 -m pip install scipy  # On Linux, Mac OS X
py -3 -m pip install scipy    # On Windows
numpy for creating and modifying ndarrays of data
To install numpy run the following:
python3 -m pip install numpy  # On Linux, Mac OS X
py -3 -m pip install numpy    # On Windows
Cython for the cythonized kendall_dis method
To install the Cython Python library run the following:
python3 -m pip install Cython  # On Linux, Mac OS X
py -3 -m pip install Cython    # On Windows

WARNING- If the following pip error message is generated, then the python3 devel package must be installed:

"fatal error: Python.h: No such file or directory"

Basic usage¶

To use the icikt package, input a 2d array with n columns each representing an array of data for a variable. The iciktArray will return two n x n 2d arrays for correlations and p-values. Each element will correspond to the result of a combination of two columns in the input array. iciktArray can also be called from the command-line interface given the file path for the data along with several optional parameters(more in docs/tutorial).

Running through command line :

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

Running through python script :

import numpy as np
import icikt

dataArray = np.genfromtxt('/path/to/file.tsv', delimiter="\t")
# or with random values
dataArray = numpy.random.randn(100, 2)

# running just 2 arrays with icikt
corr, pVal, tMax = icikt.icikt(dataArray[:,0], dataArray[:,1])

# running all combinations with iciktArray
scaled, corrRaw, pVals, tauMax = icikt.iciktArray(dataArray)

License¶

A modified Clear BSD License

Redistribution and use in source and binary forms, with or without modification, are permitted (subject to the limitations in the disclaimer below) provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
If the source code is used in a published work, then proper citation of the source code must be included with the published work.

NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY’S PATENT RIGHTS ARE GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

The icikt API Reference¶

Python Information-Content-Informed Kendall Tau Correlation (ICIKT)¶

The icikt package provides a Python tool to calculate an information-content-informed Kendall Tau correlation coefficient between arrays, while also handling missing values or values which need to be removed.

icikt.methods.icikt(x: ndarray, y: ndarray, perspective: str = 'global') → tuple[source]¶

Finds missing values, and replaces them with a value slightly smaller than the minimum between both arrays.

Parameters

x – First array of data
y – Second array of data
perspective – perspective can be ‘local’ or ‘global’. Default is ‘global’. Global includes (NA,NA) pairs in the calculation, while local does not.

Returns

tuple with correlation, pvalue, and tauMax values

icikt.methods.iciktArray(dataArray: ndarray, globalNA: float = 0, perspective: str = 'global', scaleMax: bool = True, diagGood: bool = True, includeOnly: Optional[tuple] = None) → tuple[source]¶

Calls iciKT to calculate ICI-Kendall-Tau between every combination of columns in the input 2d array, dataArray. Also replaces any instance of the globalNA in the array with np.nan.

Parameters

dataArray – 2d array with columns of data to analyze
globalNA – Optional value to replace with np.nan. Default is 0.
perspective – perspective can be ‘local’ or ‘global’. Default is ‘global’. Global includes (NA,NA) pairs in the calculation, while local does not.
scaleMax – should everything be scaled compared to the maximum correlation?
diagGood – should the diagonal entries reflect how many entries in the sample were “good”?
includeOnly – only run correlations of specified columns/combinations

Returns

tuple of the output correlations, raw correlations, pvalues, and max tau 2d arrays

Future Parameters: featureNA sampleNA

icikt.kendall_dis.kendall_dis(x, y)[source]¶

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.py -h

Usage:
    icikt.py iciktArray <dataFilePath> [--data-format=<format>] [--replace=<globalNA>] [--mode=<perspective>] [--scale=<scaleMax>] [--diag=<diagGood>]
    icikt.py -h | --help

Using a csv file with no global replace values:

icikt.py iciktArray test.csv --data-format=csv --replace=None

Using a tsv file with no global replace values:

icikt.py iciktArray test.tsv --data-format=tsv --replace=None

Using a csv file with 0 as the replace value:

icikt.py iciktArray test.csv --data-format=csv

Using a csv file in local mode with 0 as the replace value:

icikt.py iciktArray test.csv --mode=local --data-format=csv

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=',')

Welcome to icikt’s documentation!¶

icikt¶

Description¶

Installation¶

Install on Linux, Mac OS X¶

Install on Windows¶

Upgrade on Linux, Mac OS X¶

Upgrade on Windows¶

Get the source code¶

Dependencies¶

Basic usage¶

License¶

Documentation index:¶

icikt¶

Description¶

Installation¶

Install on Linux, Mac OS X¶

Install on Windows¶

Upgrade on Linux, Mac OS X¶

Upgrade on Windows¶

Get the source code¶

Dependencies¶

Basic usage¶

License¶

The icikt API Reference¶

Python Information-Content-Informed Kendall Tau Correlation (ICIKT)¶

The icikt Tutorial¶

Importing icikt package¶

Using icikt in the command-line interface¶

Using icikt in a Python script¶

Indices and tables¶