plotGenome: Visualize genome-wide PAF alignments.

In daewoooo/SVbyEye: Visualization of genomic structural variants

Visualize genome-wide PAF alignments.

Description

This function takes genome-wide alignments of de novo assembly to the reference genome PAF format and visualize the alignments with respect to all reference chromosomes in a single plot

Usage

plotGenome(
  paf.table,
  min.deletion.size = NULL,
  min.insertion.size = NULL,
  highlight.sv = NULL,
  binsize = NULL,
  color.by = "direction",
  color.palette = NULL,
  perc.identity.breaks = c(90, 95, 99, 99.5, 99.6, 99.7, 99.8, 99.9),
  chromosomes = NULL,
  chromosome.bar.width = grid::unit(2, "mm"),
  min.query.aligned.bp = NULL,
  genomic.scale = "bp",
  target.centromeres = NULL
)

Arguments

paf.table	A data.frame or tibble containing a single or multiple PAF record(s) with 12 mandatory columns along with CIGAR string defined in 'cg' column.
min.deletion.size	A minimum size (in base pairs) of a deletion to be retained.
min.insertion.size	A minimum size (in base pairs) of an insertion to be retained.
highlight.sv	Visualize alignment embedded structural variation either as an outlined ('outline') or filled ('fill') miropeats.
binsize	A size of a bin in base pairs to split a PAF alignment into.
color.by	Color alignments either by directionality ('direction'), fraction of matched base pairs ('identity'), or a custom column name present in submitted 'paf.table'.
color.palette	A discrete color palette defined as named character vector (elements = colors, names = discrete levels) to color alignment directionality, ‘[default: color.palette <- c(’-' = 'cornflowerblue', '+' = 'forestgreen')]'.
perc.identity.breaks	Set of percentage values to categorize alignment percent identity into a set of discrete colors.
chromosomes	User defined chromosomes (target sequence IDs) to be plotted.
chromosome.bar.width	A width of chromosome/contig bars over each alignment '[Default : 2mm]'.
min.query.aligned.bp	Only contigs with this minimum number of aligned base pairs will be plotted.
genomic.scale	Report genomic coordinates in base pairs ('bp') kilobase pairs ('kbp') or megabase pairs ('Mbp') ‘[default: ’bp']'.
target.centromeres	A GRanges-class object containing positions of centromeres in target chromosomes.

Value

A ggplot2 object.

Author(s)

David Porubsky

Examples

## Get PAF to plot ##
paf.file <- system.file("extdata", "PTR_test.paf", package = "SVbyEye")
## Read in PAF
paf.table <- readPaf(paf.file = paf.file)
## Make a plot ##
## Color by alignment directionality
plotGenome(
    paf.table = paf.table, chromosome.bar.width = grid::unit(2, "mm"),
    min.query.aligned.bp = 5000000
)

daewoooo/SVbyEye documentation built on Oct. 15, 2024, 6:12 a.m.