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)

[Package fabia version 2.38.0 Index]