fabia (version 2.18.0)

plotBicluster: 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.

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)