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Old 12-30-2013, 12:30 AM   #1
pirates.genome
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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

etc....

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
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cnv, ggbio, ggplot, heatmap

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