rphast (version 1.0)

plot.gene: Gene plot

Description

make gene plot

Usage

plot.gene(x, y=0, height=1, arrow.density=5, angle=30, col="black",
    lty=par("lty"), lwd=par("lwd"), add=FALSE, xlim=range.feat(x),
    ylim=c(y - height * 3/4, y + height * 3/4), ...)

Arguments

x

An object of type feat

y

the location of the plot on the y axis

height

the height of the boxes

arrow.density

The density of the arrows in arrows per inch

angle

angle (in degrees) of the arrow heads

col

color to use for plotting

lty

line type for arrows, borders, and shading

lwd

line width for arrows, borders and shading

add

if TRUE, add to existing plot

xlim

A numerical vector of length 2 giving the range for the x-axis.

ylim

A numerical vector of length 2 giving the range for the y-axis.

...

graphical parameters to be passed to plot.

Examples

exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
featFile <- "sol1.gp"
unzip(exampleArchive, featFile)
f <- read.feat(featFile)
plot.gene(f)
plot.gene(f, xlim=c(0, 10000))  #zoom in