plot method for SeqDiff object

# S4 method for SeqDiff,ANY
plot(
  x,
  width = 50,
  title = "auto",
  xlab = "Nucleotide Position",
  by = "bar",
  fill = "firebrick",
  colors = c(A = "#ff6d6d", C = "#769dcc", G = "#f2be3c", T = "#74ce98"),
  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

Author

guangchuang yu

Examples

fas <- list.files(system.file("extdata", "GVariation", package="ggmsa"),
                  pattern="fas", full.names=TRUE)
x1 <- seqdiff(fas[1], reference=1)
plot(x1)