plot-methods: plot method for SeqDiff object

In YuLab-SMU/ggmsa: Plot Multiple Sequence Alignment using 'ggplot2'

plot method for SeqDiff object

Description

plot method for SeqDiff object

Usage

## S4 method for signature '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(s)

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)

YuLab-SMU/ggmsa documentation built on Dec. 18, 2024, 11:53 p.m.