pafr (version 0.0.2)

dotplot: Generate a dot plot from a paf alignment

Description

Generate a dot plot from a paf alignment

Usage

dotplot(
  ali,
  order_by = c("size", "qstart", "provided"),
  label_seqs = FALSE,
  dashes = TRUE,
  ordering = list(),
  alignment_colour = "black",
  xlab = "query",
  ylab = "target",
  line_size = 2
)

Arguments

ali

pafr or tibble containing the genome alignment (as returned by read_paf)

order_by

How the query and target sequences should be ordered in the dot plot. Option must be one of 'size' (smallest-to-largest), 'qstart' (query organised smallest to largest, target by first match in the query genome) or 'provided' (ordering as specified in the ordering argument)

label_seqs

boolean If TRUE, label centre of query and target sequences in margins of the dot plot

dashes

boolean If TRUE, add dashes to borders of query and target sequences in the dot plot

ordering

If order_by is set to TRUE, this variable should be a list with two elements specifying the order of query and then target sequences in the dot plot. This option is ignored if order_by is set to other values

alignment_colour

character The colour used to draw each aligned section in the dot plot (defaults to black)

xlab

character The x-axis label (defaults to 'query')

ylab

character The y-axis label (defaults to 'target')

line_size

The width of the line used to represent an alignment in the dot plot (defaults to 2)

Examples

# NOT RUN {
ali <- read_paf( system.file("extdata", "fungi.paf", package="pafr") )
dotplot(ali)
dotplot(ali) + theme_bw()
dotplot(ali, label_seqs=TRUE, order_by="qstart", alignment_colour="blue")
# }