LinChange

Investigating the linear correlation between two variables is a standard procedure for analysing genomic data. This helper script in Python provides a command line interface for producing pretty plots for the linear dependency.

Requirements and Installation

The script is written in Python3 (Python 3.6 or larger is recommended). Moreover, the necessary libraries are installed with pip. Run

python3 -m pip install requirements.txt

Usage

Run

python3 linchange.py [data_paths] --annotation=path/to/bed/or/gtf [-n name1 -n name2]  --title=Title --distinguish_strand --percentile=100 --save_fig --save_path=path/to/saved/figure.png

with

• data_paths: 2 or 4 data paths to the bigwig files. If 4 paths are passed, the first two and the second two are added together (e.g. + strand and - strand of WT and mutant).
• --bed: path to the annotation bed file.
• -n: that are printed on the plots axes. The first names is used for the x-axis, whilst the second name is used for the y-axis.
• --title or -t: plot title.
• --distinguish_strand: if set, two consecutive strands are considered as + and - (in that order)
• --percentile: Only keep the lower percentile.
• --save_fig: If set, figure is set to file at save_path
• --save_path: Figures is saved under this file name if save_fig is set.