CaNVAS_CNV

This folder contains the scripts for processing and plotting of the CaNVAS CNV files.

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Installation and Set-up

To create and acivate a conda environment in which to run the scripts use the following command. If you do not want to use conda, skip to the section labeled installing packages without conda.

conda create -n CaNVAS_CNV python=3.9
activate CaNVAS_CNV

Then, install the following packages needed for the scripts.

conda install -c plotly plotly
conda install pandas
conda install numpy

To install python packages without the use of conda, use the following commands:

pip install plotly
pip install pandas
pip install numpy

Running CaNVAS_CNV

To run the CaNVAS CNV processing script use the following syntax:

./process_CaNVAS_CNV.py -infile list_CNV_areas -inpath path_to_genetic_data -outfile output_filename -outpath output_path

The following arguments are required to sucessfully run the script: -infile A file containing the CNV areas. This file should have the columns "Chr CNVStart CNVEnd LeftStart LeftEnd RightStart RightEnd" and be tab delimited. -inpath The path to a folder with genotype data for processing. One file of genotype data should be provided for each individual. -outfile The name you would like for the output files -outpath The path to where the output files should be written

The CaNVAS CNV script will create one output file for each CNV with the relevant information listed fore each individual for that CNV. The script will also create a folder within the output path that can be used for plotting later. The script has run properly if you see a list of individual names slowly writing to the screen and the output path is created and filled.

Plotting output data

After running the process_CaNVAS_CNV.py script, you may want to plot your data. To do so you can use one of the plotting scripts provided. use the plotCaNVAS.py script.

All scripts use the same syntax. Example syntax for the plotCanVAS.py script is shown below.

./plotCaNVAS.py -path output_path_containing_CNV_files

The -path argument is required and the output path from the process_CaNVAS_CNV.py file above or the path to a folder with the processed CNV files (not plots) should be provided.

This script should automatically generate a set of interactive HTML plots for each CNV. The plots generated will depend on the script chosen.

The default plotting script uses Mean as the independent and dependent variable by default. If you would like to plot Medians, please use the script plotCaNVAS_Medians.py. Scripts plotting normalization of either the mean or median values are also provided.