R/mismatch-plot.R

In julian-gehring/Rariant: Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies

tallyPlot <- function(file, region, ref, nCycles = 0, minQual = 0, minFreq = 0, ...) {

    n = width(region)
    
    tally = tallyBamRegion(file, region, nCycles, minQual)
    #tally = selectStrand(tally, "both")
    colnames(tally) = c("A", "C", "G", "T")
    
    ref = ds2int(getSeq(ref, region)[[1]])
    
    ## add 'N/R' base to tally
    tally = cbind(tally, N = tally[cbind(1:n, ref)])
    tally[cbind(1:n, ref)] = 0
    
    d = melt(tally)
    #dn = subset(d, value > 0) ## causes NOTE in check
    dn = d[d$value > 0, ]
    
    gn = GRanges(seqnames(region),
        IRanges(start(region):end(region), width = 1))
    gx = gn[dn$Var1]
    gx$base = dn$Var2
    gx$count = dn$value
    #gx = sort(gx)
        
    p = autoplot(gx,
        aes_string(x = "start", y = "count", fill = "base"),
        stat = "identity",
        position = "stack",
        geom = "bar",
        width = 1, ...)
    p = p + baseFillScale() + theme_bw()
    
    return(p)
}