Plot synteny between a query and target sequence in a PAF alignment

Plot synteny between a query and target sequence in a PAF alignment

plot_synteny(
  ali,
  q_chrom,
  t_chrom,
  centre = TRUE,
  rc = FALSE,
  xlab = "Position in query",
  ylab = "",
  x_labeller = Mb_lab
)

Arguments

ali	pafr or tibble containing the genome alignment (as returned by read_paf)
q_chrom	character Name for the query sequence
t_chrom	character Name for the target sequence
centre	logical If TRUE (default), adjust the position of the target sequence, so it is centred on the query. If not, both sequences start at position zero
rc	logical If TRUE, use the reverse and complement for the target sequence
xlab	string Name for the x-axis
ylab	string Name for the y-axis
x_labeller	Function to be used to label the x-axis

Value

A ggplot object that displays synteny between query and target sequences

Examples

ali <- read_paf( system.file("extdata", "fungi.paf", package="pafr") )
long_ali <- subset(ali, alen > 1e4)
plot_synteny(long_ali, q_chrom="Q_chr3", t_chrom="T_chr4", centre=TRUE)
plot_synteny(long_ali, q_chrom="Q_chr5", t_chrom="T_chr5", centre=TRUE)
plot_synteny(long_ali, q_chrom="Q_chr5", t_chrom="T_chr5", centre=TRUE, rc=TRUE)