GenomePlot {aCGH.Spline}R Documentation

Produces a genome plot.

Description

Create a plot of the genome - plots each chromosome separately on the same figure.

Usage

GenomePlot(x, ylim=c(-3,3), axes=FALSE, pch=46, col="black")

Arguments

x - a ".temp" formatted data stucture.
ylim - the y-axis limits defaults to c(-3,3).
axes - should axes be draw around each plot (TRUE or FALSE).
pch - the point character to use defaults to 46.
col - the point color defaults to "black".

Details

Plots as many chromosome as are contained within the ".temp" formatted data stucture on the same figure.

Value

A plot showing each chromosome separatly.

Author(s)

Tomas William Fitzgerald

Examples


# Create a vector of chromosome numbers
chr = rnorm(100,1,0)
for (x in 2:24) { 
        chr = c(chr, rnorm(100,x,0)) 
}

# Create a ".temp" data structure
mat = matrix(ncol=8, nrow=length(chr))
mat[,1] = log2(rnorm(length(chr),1000,150)/rnorm(length(chr),800,180))
mat[,2] = rnorm(length(chr),1000,150)
mat[,3] = rnorm(length(chr),800,180)
mat[,4] = chr
mat[,5] = seq(1,length(chr), 1)
mat[,6] = seq(1,length(chr), 1)
mat[,7] = 0
mat[,8] = 0

# Plot the data
GenomePlot(mat)


[Package aCGH.Spline version 2.2 Index]