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  • 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 Files
    Last edited by pirates.genome; 12-30-2013, 03:01 AM. Reason: added the input data

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