plotBicluster {fabia}

R Documentation

Plotting of a bicluster

Description

plotBicluster: R implementation of plotBicluster.

Usage

plotBicluster(r,p,opp=FALSE,zlim=NULL,title=NULL,which=c(1, 2))

Arguments

r	the result of extract_bic.
p	the bicluster to plot.
opp	plot opposite bicluster, default = FALSE.
zlim	vector containing a low and high value to use for the color scale.
title	title of the plot.
which	which plots are shown: 1=data matrix with bicluster on upper left, 2=plot of the bicluster; default c(1, 2).

Details

One bicluster is visualized by two plots. The variable "which" indicates which plots should be shown.

Plot1 (which=1): The data matrix is sorted such that the bicluster appear at the upper left corner. The bicluster is marked by a rectangle.

Plot2 (which=2): Only the bicluster is plotted.

Implementation in R.

Value

Plotting of a bicluster

Author(s)

Sepp Hochreiter

See Also

fabia, fabias, fabiap, fabi, fabiasp, mfsc, nmfdiv, nmfeu, nmfsc, extractPlot, extractBic, plotBicluster, Factorization, projFuncPos, projFunc, estimateMode, makeFabiaData, makeFabiaDataBlocks, makeFabiaDataPos, makeFabiaDataBlocksPos, matrixImagePlot, fabiaDemo, fabiaVersion

Examples

#---------------
# TEST
#---------------

dat <- makeFabiaDataBlocks(n = 100,l= 50,p = 3,f1 = 5,f2 = 5,
  of1 = 5,of2 = 10,sd_noise = 3.0,sd_z_noise = 0.2,mean_z = 2.0,
  sd_z = 1.0,sd_l_noise = 0.2,mean_l = 3.0,sd_l = 1.0)

X <- dat[[1]]
Y <- dat[[2]]


resEx <- fabia(X,3,0.01,20)

rEx <- extractBic(resEx)

plotBicluster(rEx,p=1)


## Not run: 
#---------------
# DEMO1
#---------------

dat <- makeFabiaDataBlocks(n = 1000,l= 100,p = 10,f1 = 5,f2 = 5,
  of1 = 5,of2 = 10,sd_noise = 3.0,sd_z_noise = 0.2,mean_z = 2.0,
  sd_z = 1.0,sd_l_noise = 0.2,mean_l = 3.0,sd_l = 1.0)

X <- dat[[1]]
Y <- dat[[2]]


resToy <- fabia(X,13,0.01,200)



rToy <- extractBic(resToy)

plotBicluster(rToy,p=1)

#---------------
# DEMO2
#---------------

avail <- require(fabiaData)

if (!avail) {
    message("")
    message("")
    message("#####################################################")
    message("Package 'fabiaData' is not available: please install.")
    message("#####################################################")
} else {

data(Breast_A)

X <- as.matrix(XBreast)

resBreast <- fabia(X,5,0.1,200)

rBreast <- extractBic(resBreast)

plotBicluster(rBreast,p=1)

}


## End(Not run)

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