View Single Post
Old 12-30-2013, 12:30 AM   #1
Location: Earth

Join Date: Mar 2012
Posts: 11
Question visualization of CNV with genomic coordinates in R ggplot2 or ggbio

Hi all,

I came through a heatmap of CNVs from Illumina Genome Studio which has four samples (see attachment). On Y axis they have genomic coordinates and on X axis the samples. Red denotes amplification and blue denotes deletion. I was wondering how can we make similar heatmap in R for CNV data or expression data? I know a little basis of ggplot and ggbio but I don't know how to make heatmap with genomic coordinates on Y axis.
CNV data is in segments:

chr start end copy-number
chr1 23432 25925 4
chr2 1375364 1378364 1


Thanks in advance.
Attached Images
File Type: jpg CNV heatmap.jpg (31.1 KB, 34 views)

Last edited by pirates.genome; 12-30-2013 at 02:01 AM. Reason: added the input data
pirates.genome is offline   Reply With Quote