spotSegmentation (version 1.46.0)

plot.spotseg: Microarray Spot Segmentation Plot

Description

Plot method for the spotseg function. Displays the result obtained from microarray spot segmentation via model-based clustering.

Usage

"plot"(x,...)

Arguments

x

An object of class "spotseg", which is the output of the function spotseg.

...

Unused but required by generic "plot" method.

Value

References

Q. Li, C. Fraley, R. Bumgarner, K. Y. Yeung, and A. Raftery\ Robust model-based segmentation of microarray images,\ Technical Report No.~473, Department of Statistics, University of Washington, January 2005.

See Also

spotseg

Examples

data(spotSegTest)

# columns of spotSegTest:
#  1 intensities from the Cy3 (green) channel
#  2 intensities from the Cy5 (red) channel

dataTransformation <- function(x) (256*256-1-x)^2*4.71542407E-05 

chan1 <- matrix(dataTransformation(spotSegTest[,1]), 144, 199)
chan2 <- matrix(dataTransformation(spotSegTest[,2]), 144, 199)

hivGrid <- spotgrid( chan1, chan2, rows = 4, cols = 6, show = TRUE)

library(mclust)

hivSeg <- spotseg( chan1, chan2, hivGrid$rowcut, hivGrid$colcut)

plot(hivSeg)