README.md

scCNV_heatmap 1.3.1 - plotting a ploidy sorted heatmap from scCNV data (10x Genomics)

Python 3
Dependencies: csv, argparse, cairosvg
This program is a little memory hungry...

Note: Current version uses the GRCh37 (hg19) genome. If a different species or genome build is desired, 
the "chromosome_sizes" list can be adjusted in the python skript.

A bar with ploidies will be plotted on the right side of the heatmap.

Usage:
-o  Output filename
-c  node_unmerged_cnv_calls.bed file from the 10x pipeline output
-p  per_cell_summary_metrics.csv file from the 10x pipeline output

Optional:
-e  Set to "no" to include noisy cells marked by the 10x pipeline. Default is "yes"
-f  Set a lower ploidy cuttoff if desired. E.g "-f 1.1" will exclude all cells with a ploidy lower than 1.1