stabpath: Stability paths plot

In s4vd: Biclustering via Sparse Singular Value Decomposition Incorporating Stability Selection

Description

The function plots the stability path of a S4VD result

Usage

stabpath(res,number)

Arguments

res	the S4VD result
number	the bicluster for which the stability path shall be plotted

Details

Plots the stability path for the rows and the columns regarding the last iteration of the s4vd algorithm. Note that if the pointwise error control was used or if savepath=FALSE the final selection probabilities for the rows and the columns will be plotted.

Author(s)

Martin Sill \ [e-mail]

Examples

# example data set according to the simulation study in Lee et al. 2010
# generate artifical data set and a correspondig biclust object
u <- c(10,9,8,7,6,5,4,3,rep(2,17),rep(0,75))
v <- c(10,-10,8,-8,5,-5,rep(3,5),rep(-3,5),rep(0,34))
u <- u/sqrt(sum(u^2)) 
v <- v/sqrt(sum(v^2))
d <- 50
set.seed(1)
X <- (d*u%*%t(v)) + matrix(rnorm(100*50),100,50)
params <- info <- list()
RowxNumber <- matrix(rep(FALSE,100),ncol=1)
NumberxCol <- matrix(rep(FALSE,50),nrow=1)
RowxNumber[u!=0,1] <- TRUE 
NumberxCol[1,v!=0] <- TRUE
Number <- 1
ressim <- BiclustResult(params,RowxNumber,NumberxCol,Number,info)
#perform s4vd biclustering 
ress4vd <- biclust(X,method=BCs4vd,pcerv=0.5,
                        pceru=0.5,ss.thr=c(0.6,0.65),steps=500,
                        pointwise=FALSE,nbiclust=1,savepath=TRUE)
#perform s4vd biclustering with fast pointwise stability selection
ress4vdpw <- biclust(X,method=BCs4vd,pcerv=0.5,
                          pceru=0.5,ss.thr=c(0.6,0.65),steps=500,
                          pointwise=TRUE,nbiclust=1)
#stability paths
stabpath(ress4vd,1)
#selection probabilitys for the pointwise stability selection
stabpath(ress4vdpw,1)

s4vd documentation built on May 2, 2019, 4:47 p.m.