highlight_dotplot: Highlight segments of a query or target genome in a dot plot
In dwinter/pafr: Read, Manipulate and Visualize 'Pairwise mApping Format' Data

This plot is intended to be used in conjunction with link{dotplot}. Adding higlight_query or highlight_target to a dotplot function call (see examples below) will add a rectangular 'highlight' corresponding to a particular genomic interval in the corresponding genome.

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highlight_query(bed, fill = "yellow", colour = "black", alpha = 0.6)

highlight_target(bed, fill = "yellow", colour = "black", alpha = 0.6)

`bed`	`data.frame` or `tbl_df` containing a bed file, as returned by `read_bed`. Should contain three columns named 'chrom', 'start' and 'end'
`fill`	character Fill colour for highlight segment
`colour`	character Outline colour for highlight segment
`alpha`	character Opacity ([0-1]) for highlight segment

ali <- read_paf( system.file("extdata", "fungi.paf", package="pafr") )
cen <- read_bed(system.file("extdata", "Q_centro.bed", package="pafr"))
dotplot(ali) + highlight_query(cen)
interval <- data.frame(chrom="T_chr3", start=2000000, end=3000000)
dotplot(ali, label_seqs=TRUE) + 
   highlight_target(interval)