plot_synteny {pafr}

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

Description

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

Usage

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)