seq2R (version 2.0.1)

plot.change.points: Visualization of change.points objects

Description

Useful for drawing the estimation and first derivative of the skew profile.

Usage

# S3 method for change.points
plot(x = model, y = NULL, base.pairs = NULL, der = NULL,
xlab = "x", ylab = "y", col = "black", CIcol = "black", main = NULL, type = "l",
CItype = "l", critical = FALSE, CIcritical = FALSE,ylim=NULL,...)

Value

Simply produce a plot.

Arguments

x

change.points object.

y

NULL

base.pairs

Character string about the skew profile for A vs. T or C vs. G.

der

Number which determines inference process to be drawing into the plot. By default der is NULL. If it is 0, the plot represents the initial estimate. If der is 1, the first derivative is plotted.

xlab

Title for x axis.

ylab

Title for y axis.

col

A specification for the default plotting color.

CIcol

A specification for the default confidence intervals plotting color.

main

An overall title for the plot.

type

Type of plot should be drawn. Possible types are, p for points, l for lines, o for overplotted, etc. See details in ?par.

CItype

Type of plot should be drawn for confidence intervals. Possible types are, p for points, l for lines, o for overplotted, etc. See details in ?par.

critical

A logical value. If TRUE (not by default), the critical points are drawn into the plot.

CIcritical

A logical value. If TRUE (not by default), the 95% confidence intervals for the critical points are drawn into the plot.

ylim

The y limits of the plot.

...

Other options.

Author

Nora M. Villanueva and Marta Sestelo.

Examples

library(seq2R)


#mtDNAhum <- read.genbank("NC_012920")
data(mtDNAhum)
DNA <- transform(mtDNAhum)
seq1 <- find.points(DNA)



plot(seq1,der=0,base.pairs="CG",CIcritical=TRUE,ylim=c(0.08,0.67))
plot(seq1,der=1,base.pairs="CG",CIcritical=TRUE,ylim=c(-0.0005,0.00045))
abline(h=0)



plot(seq1,critical=TRUE, CIcritical=TRUE)