Usage
Installation
Use the package manager [pip](https://pip.pypa.io/en/stable/) to install CHESSBOARD and the API.
$ pip install git+https://bitbucket.org/biociphers/chessboard
Usage
CHESSBOARD is a command line tool that can be run as follows using the provided arguments. Note that the input is a
CHESSBOARD .cb
file which can be generated using our API. The API allows the user to import raw data for processing
prior to running CHESSBOARD and explore the algorithm output for downstream analsysis.
usage: chessboard [-h] [-A CONC] [-L REG] [-I ITER] [-B BURNIN] [-T THIN]
[-S BLOCKSIZE] [-M minsize] [-K kinit] [-V verbose] [--version]
input out_dir
positional arguments:
input Path to the chessboard input file.
out_dir Path to the output directory; will be created if it
does not already exist.
optional arguments:
-h, --help show this help message and exit
-A CONC, --conc CONC Concentration parameter. Larger values increase the
number of learned clusters. (default: 1e-100)
-L REG, --reg REG Regularization parameter. (default: 50)
-I ITER, --iter ITER Number of iterations to run the Gibbs sampler.
(default: 1000)
-B BURNIN, --burnin BURNIN
Number of burn-in iterations. (default: 200)
-T THIN, --thin THIN Number of samples to discard between iterations to
reduce autocorrelation. (default: 2)
-S BLOCKSIZE, --blocksize BLOCKSIZE
Maximum block size for blocked Gibbs sampling
procedure. (default: 10)
-M MINSIZE, --minsize MINSIZE
Minimum tile size. (default: 20)
-K KINIT, --kinit KINIT
Number of clusters for k-means initialization. (default: 5)
-V, --verbose
Verbose mode. (default: False)
--version show program's version number and exit