biclustmember {biclust}R Documentation

Bicluster Membership Graph

Description

Draws a membership graph cluster x columns

Usage

biclustmember(bicResult, x, mid = T, cl_label = "", which=NA, 
  main = "BiCluster Membership Graph", xlab="Cluster", 
  color=diverge_hcl(101, h = c(0, 130)), ...)

clustmember(res, x, mid = T, cl_label = "", which=NA, 
  main = "Cluster Membership Graph", xlab="Cluster", 
  color=diverge_hcl(101, h = c(0, 130)), ...)

bicorder(bicResult, cols=TRUE, rev=FALSE)

Arguments

x

The data matrix

bicResult

BiclustResult object with a bicluster result set.

res

Cluster Result (is converted into a kcca object)

mid

If TRUE, shows the value of the remaining objects inside the cluster value, else shows both aside each other.

cl_label

Ticks of x-axis

which

If specified gives the ploting order of the columns from bottom to top

main

Gives the title of the plot

xlab

Label of x-axis

color

Range of colors for the plot

...

Additional plot options or if neccessary option for as.kcca

cols

If TRUE orders the column by appearance in the bicluster, else orders the rows.

rev

If TRUE reverses the order

Author(s)

Sebastian Kaiser sebastian.kaiser@stat.uni-muenchen.de

See Also

bubbleplot for simultaneous representation of biclusters, parallelCoordinatesfor single representation of biclusters as lines of gene or condition profiles, drawHeatmapfor Heatmap representation of biclusters and biclustbarchart for a barchart.

Examples

  set.seed(1)
  x=matrix(rnorm(900),30,30)
  x[1:5,1:5]=rnorm(25,3,0.3)
  x[11:15,11:15]=rnorm(25,-3,0.3)
  x[21:25,21:25]=rnorm(25,6,0.3)
  colnames(x)<-paste("Var.",1:30)
  bics <- biclust(x,BCPlaid(), back.fit = 2, shuffle = 3, fit.model = ~m + a + b,
  iter.startup = 5, iter.layer = 30,  verbose = TRUE)
  
  biclustmember(bics,x)
  
  ord<-bicorder(bics, cols=TRUE, rev=TRUE)
  
  biclustmember(bics,x,which=ord)
  


[Package biclust version 2.0.3 Index]