In the output of GISTIC2.0 algorithm for copy number analysis, there is a generated heatmap Segmented Copy Number (raw_copy_number.pdf and raw_copy_number.png).
The png file is shown as the following:
This file is a heat map image of the segmented copy number profiles in the input data.
Now I get all the output file from GISTIC2.0, and I would like to reproduce this file in R by my side. My questions are:
1) Which file should be the input, all_data_by_genes.txt or broad_data_by_genes.txt? Is there any normalization should be made first to plot this heatmap?
2) How to generate chromosome coordinates along with the heatmap (see the left annotation of chromosome)?
Many thanks advanced!