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

In pafr: Read, Manipulate and Visualize 'Pairwise mApping Format' Data

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

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)

pafr documentation built on Dec. 8, 2020, 5:06 p.m.