clustmember: Bicluster Membership Graph

In biclust: BiCluster Algorithms

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 [e-mail]

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)
  

biclust documentation built on May 31, 2023, 6:18 p.m.