pafr (version 0.0.2)

highlight_query: Highlight segments of a query or target genome in a dot plot

Description

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.

Usage

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

Arguments

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

Examples

# NOT RUN {
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)
# }