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]