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-   -   visualization of CNV with genomic coordinates in R ggplot2 or ggbio (http://seqanswers.com/forums/showthread.php?t=39539)

pirates.genome 12-30-2013 12:30 AM

visualization of CNV with genomic coordinates in R ggplot2 or ggbio
 
1 Attachment(s)
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. :)


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