Question: Heatmap for GISTIC2.0
gravatar for sugus
10 weeks ago by
China Pharmaceutical University
sugus40 wrote:

Hi there,

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: heatmap

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!

heatmap gistic2.0 cnv R • 176 views
ADD COMMENTlink modified 11 days ago by Biostar ♦♦ 20 • written 10 weeks ago by sugus40
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