R/kataegisPlot.R

In seandavi/MutationTools: What the package does (short line)

#' Make a kataegis plot from a set of variants
#' 
#' @importFrom Biostrings complement
kataegisPlot <- function(vcf) {
    vcfsimple = vcf[isSNV(vcf)]
    d = distanceToPreviousVariant(vcfsimple)
    vardf = GRanges(seqnames=seqnames(vcfsimple),ranges=ranges(vcfsimple),
        ref = DNAStringSet(ref(vcfsimple)),
        alt = DNAStringSet(unlist(alt(vcfsimple))[start(PartitioningByEnd(alt(vcfsimple)))]))
    mcols(vardf)$alt[mcols(vardf)$ref %in% c('G','T')] = complement(mcols(vardf)$alt[mcols(vardf)$ref %in% c('G','T')])
    mcols(vardf)$ref[mcols(vardf)$ref %in% c('G','T')] = complement(mcols(vardf)$ref[mcols(vardf)$ref %in% c('G','T')])
    x = data.frame(mutation=paste(mcols(vardf)$ref,mcols(vardf)$alt,sep=" > "),
        distance=d)
    ggplot(x,aes(x=seq_along(distance),y=distance)) + geom_point(aes(color=mutation)) + scale_y_log10()
}