plotMiro: Visualize PAF alignments.
In daewoooo/SVbyEye: Visualization of genomic structural variants

plotMiro

R Documentation

Visualize PAF alignments.

Description

This function takes PAF output file from minimap2 alignments, and visualize the alignments in a miropeat style.

Usage

plotMiro(
  paf.table,
  min.deletion.size = NULL,
  min.insertion.size = NULL,
  highlight.sv = NULL,
  binsize = NULL,
  color.by = "direction",
  perc.identity.breaks = c(90, 95, 99, 99.5, 99.6, 99.7, 99.8, 99.9),
  color.palette = NULL,
  outline.alignments = FALSE,
  offset.alignments = FALSE,
  add.alignment.arrows = TRUE,
  target.region = NULL,
  genomic.scale = "bp"
)

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'.
`perc.identity.breaks`	Set of percentage values to categorize alignment percent identity into a set of discrete colors.
`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')]'.
`outline.alignments`	Set to `TRUE` if boundaries of each alignment should be highlighted by gray outline.
`offset.alignments`	Set to `TRUE` if subsequent target alignments should be offsetted below and above the midline.
`add.alignment.arrows`	Set to `FALSE` if alignment arrows should not be added to the plot.
`target.region`	A user defined target region either as character string ('chr:start-end') or as a `GRanges-class` object containing a single genomic region to which PAF alignments will be narrowed down.
`genomic.scale`	Report genomic coordinates in base pairs ('bp') kilobase pairs ('kbp') or megabase pairs ('Mbp') ‘[default: ’bp']'.

Value

A ggplot2 object

Author(s)

David Porubsky

Examples

## Get PAF to plot ##
paf.file <- system.file("extdata", "test1.paf", package = "SVbyEye")
## Read in PAF
paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")
## Optional steps include PAF filtering and flipping query coordinates
## (see filterPaf and flipPaf function documentation)
## Make a plot ##
## Color by alignment directionality
plotMiro(paf.table = paf.table, color.by = "direction")
## Color by fraction of matched bases in each alignment
plotMiro(paf.table = paf.table, color.by = "identity")
## Use custom color palette to color alignment directionality
plotMiro(paf.table = paf.table, color.palette = c("+" = "azure3", "-" = "yellow3"))
## Change genomic scale to megabase pairs
plotMiro(paf.table = paf.table, genomic.scale = "Mbp")
## Outline PAF alignments
plotMiro(paf.table = paf.table, outline.alignments = TRUE)
## Offset target PAF alignments
plotMiro(paf.table = paf.table, offset.alignments = TRUE)
## Bin PAF alignments into user defined bin and color them by sequence identity (% of matched bases)
plotMiro(paf.table = paf.table, binsize = 10000)
## Highlight structural variants
paf.file <- system.file("extdata", "test3.paf", package = "SVbyEye")
paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")
plotMiro(paf.table = paf.table, min.deletion.size = 50, highlight.sv = "outline")

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