PGX - Genome visualisation from the Progenetix project

This repository contains code and resources for visualizing different types of genome data, focussed on copy number variants (CNV). The software is mostly used for the progenetix.org visualizations; however, users can just download the package & use with their own data (though documentatuion is ... sparse).

Current implementations (in bin):

Genome arrays

• example implementations
  • arrayplotter.pl

Copy number histograms & (clustered) samples

• example implementations
  • CNVsegfilePlotter.pl
  • for progenetix and TCGA style segmentation & probe files

Example

• download PGX to whichever location (___my_path___)
• run as in example below, replacing the segment and label files with your own

cd ___my_path___/PGX/bin/
perl CNVsegfilePlotter.pl -outdir ./out -f ./data/testfile_segments.tab  -sf ./data/testfile_labels.tab -min_group_no 1

Sample profiles from Progenetix-style database

Example

• installation as above
• for more about Progenetix see
  • http://docs.progenetix.org
  • http://github.com/progenetix/schemas
  • http://github.com/progenetix/bycon

cd ___my_path___/PGX/bin/
perl CNVdbPlotter.pl -query icdom-81 -randno 500