ggmsa (version 1.0.2)

plot: plot method for SeqDiff object

Description

plot method for SeqDiff object

Usage

# S4 method for SeqDiff,ANY
plot(
  x,
  width = 50,
  title = "auto",
  xlab = "Nucleotide Position",
  by = "bar",
  fill = "firebrick",
  colors = c(A = "#E495A5", C = "#ABB065", G = "#39BEB1", T = "#ACA4E2"),
  xlim = NULL
)

Arguments

x

SeqDiff object

width

bin width

title

plot title

xlab

xlab

by

one of 'bar' and 'area'

fill

fill color of upper part of the plot

colors

color of lower part of the plot

xlim

limits of x-axis

Value

plot

Examples

# NOT RUN {
fas <- list.files(system.file("extdata", "GVariation", package="ggmsa"),
                  pattern="fas", full.names=TRUE)
x1 <- seqdiff(fas[1], reference=1)
plot(x1)
# }