drawHeatmap {biclust}R Documentation

Draw Heatmap

Description

Draws a microarray data matrix as a heatmap, with rows and colums reordered so the rows and columns of the input bicluster will be at top-left of the matrix.

Usage

drawHeatmap(x,bicResult=NULL,number=NA,local=TRUE, beamercolor=FALSE,paleta,...)
drawHeatmap2(x,bicResult=NULL,number=NA,plotAll=FALSE)

Arguments

x

The data matrix where the bicluster is to be drawn.

bicResult

BiclustResult object with a bicluster result set. If this value is set to NULL, the data matrix is drawn as a heatmap, without any reordering. Default NULL.

number

Bicluster to be drawn from the result set 'bicResult'. If bicResult is set to NULL, this value is ignored. Default NA

local

If TRUE, only rows and columns of the bicluster were drawn.

plotAll

If TRUE, all Bicluster of result set 'bicResult' were drawn.

beamercolor

If TRUE, palete colors are used.

paleta

Colors

...

Additional plot options

Details

'plotAll' only works if there is a exclusive rows and column Result!

Author(s)

Rodrigo Santamaria rodri@usal.es, Sebastian Kaiser

See Also

bubbleplot for simultaneous representation of biclusters.\ parallelCoordinatesfor single representation of biclusters as lines of gene or condition profiles.

Examples



  #Random 100x50 matrix with a single, up-regulated 10x10 bicluster
  s2=matrix(rnorm(5000),100,50)
  s2[11:20,11:20]=rnorm(100,3,0.3)
  set.seed(1)
  bics <- biclust(s2,BCPlaid(), back.fit = 2, shuffle = 3, fit.model = ~m + a + b,
  iter.startup = 5, iter.layer = 30,  verbose = TRUE)
  drawHeatmap(s2,bics,1)


[Package biclust version 2.0.3 Index]