dotplot {pafr} | R Documentation |
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
|
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 |
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 |
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
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")