PlotBicluster {fabia} | R Documentation

## Plotting of a bicluster

### Description

`PlotBicluster`: R implementation of `PlotBicluster`.

### Usage

    PlotBicluster(x,samples,observations,xLabels=NULL, yLabels=NULL,
    zlim=NULL, title=NULL,x11b=TRUE)

### Arguments

`x` | data matrix with columns as samples and rows as observations.
`samples` | samples beloning to the bicluster.
`observations` | observations beloning to the bicluster.
`xLabels` | vector of strings to label the columns where "samples" are a subset (default "colnames(x)").
`yLabels` | vector of strings to label the rows where "observations" are a subset (default "rownames(x)").
`zlim` | vector containing a low and high value to use for the color scale.
`title` | title of the plot.
`x11b` | screen output or not.

### Details

Plots a bicluster.

Plot1: The data matrix is sorted such that the bicluster appear at the upper left corner.

The bicluster is marked by a rectangle.

Plot2: Only the bicluster is presented.

Implementation in R.

### Author(s)

Sepp Hochreiter

### See Also

`fabi`, `fabia`, `fabiap`, `fabias`, `fabiasp`, `mfsc`, `nmfdiv`, `nmfeu`, `nmfsc`, `nprojfunc`, `projfunc`, `make_fabi_data`, `make_fabi_data_blocks`, `make_fabi_data_pos`, `make_fabi_data_blocks_pos`, `extract_plot`, `extract_bic`, `myImagePlot`, `Breast_A`, `DLBCL_B`, `Multi_A`, `fabiaDemo`, `fabiaVersion`

### Examples

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

    dat <- make_fabi_data_blocks(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,20,0.1,1.0,1.0,3)

    rEx <- extract_bic(resEx$L,resEx$Z,lapla=resEx$lapla,Psi=resEx$Psi)

    PlotBicluster(X,unlist(rEx$bic[1,5]),unlist(rEx$bic[1,3]),x11b=FALSE)

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

    dat <- make_fabi_data_blocks(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,200,0.4,1.0,1.0,13)

    rToy <- extract_bic(resToy$L,resToy$Z,lapla=resToy$lapla,Psi=resToy$Psi)

    PlotBicluster(X,unlist(rToy$bic[1,5]),unlist(rToy$bic[1,3]))

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

    data(Breast_A)

    X <- as.matrix(XBreast)

    resBreast <- fabia(X,200,0.1,1.0,1.0,5)

    rBreast <- extract_bic(resBreast$L,resBreast$Z,lapla=resBreast$lapla,Psi=resBreast$Psi)

    PlotBicluster(X,unlist(rBreast$bic[1,5]),unlist(rBreast$bic[1,3]))

    ## End(Not run)

[Package fabia version 0.1.1 Index]