image-methods: Display DNA Sequence

In haplotypes: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony

Display DNA Sequence

Description

Display an image of DNA sequences .

Usage

## S4 method for signature 'Dna'
image(x,all=FALSE,fifth=TRUE,
col=c("#BFBFBF","#0B99FD","#FD0B0B","#11A808","#F5FD0B","#F8F8FF"),
chars=TRUE,cex=1,show.names=TRUE,show.sites=TRUE,xlab="",ylab="",...)
 

Arguments

x	an object of class Dna.
all	boolean; should entire sequence be displayed or only the polymorphic sites?
fifth	boolean; if all==FALSE, should gaps be displayed?
col	an integer or character vector for the colors. By default it is blue for "A", red for "C", green for "G", yellow for "T", white for "-", and grey for "?".
chars	boolean; should characters be displayed on image?
cex	a numeric vector of expansion factor for characters.
show.names	boolean; should sequence names be displayed on the left side.
show.sites	boolean; should site labels be displayed on the bottom side.
xlab	a title for the x axis.
ylab	a title for the y axis.
...	additional arguments to image.default.

Methods

signature(x = "Dna")

Display an image of Dna objects

Author(s)

Caner Aktas, [e-mail].

See Also

image.default

Examples

data("dna.obj")
x<-dna.obj

## Display only polymorphic sites without gaps
image(x,all=FALSE,fifth=FALSE,show.names=TRUE,cex=0.6)

## Display only polymorphic sites with gaps
image(x,all=FALSE,fifth=TRUE,show.names=TRUE,cex=0.6)

## Not run: 
## Display entire sequences
image(x,all=FALSE,show.names=TRUE,cex=0.6)

## End(Not run)

haplotypes documentation built on July 26, 2023, 5:22 p.m.