bubbleplot: Bubbleplot

Description

Draws a bubble plot where each bicluster is represented as a circle (bubble). Color represents the bicluster set to which bicluster pertains (up to three bicluster sets can be represented simultaneously). Brightness represents the bicluster homogeneity (darker, less homogeneous). Size represents the size of the bicluster, as (number of genes)x(number of conditions). Location is a 2D-projection of gene and condition profiles.

Usage

bubbleplot(x, bicResult1, bicResult2=NULL, bicResult3=NULL, projection="mean", 
  showLabels=FALSE)

Arguments

x: The data matrix from which biclusters were identified.
bicResult1: BiclustResult object with a bicluster result set whose biclusters will be drawn in green.
bicResult2: BiclustResult object with an optional second bicluster result set. Will be drawn in red (default NULL)
bicResult3: BiclustResult object with an optional third bicluster result set. Will be drawn in blue (default NULL)
projection: Projection algorithm used to position bubbles. Allowed projections are 'mean', 'isomds' and 'cmdscale' (default 'mean'). See details section for a broader explanation.
showLabels: If 'TRUE', puts a label over each bubble that tells the number within the corresponding bicluster result (default 'FALSE').

Author

Rodrigo Santamaria rodri@usal.es

Details

Position of circles depend on a 2D projection of the multidimensional point formed by rows and columns present in the bicluster. For example, if we have a 3x3 matrix to analyze and we find a bicluster with rows 1 and 3 and columns 2 and 3, the corresponding multidimensional point will be p=(1,0,1,0,1,1). For this example, 'mean' projection will map the bicluster with the point x=(1+3)/2=2 and y=(2+3)/2=2,5. Other projections will take the point p and project it following the corresponding algorithms (see the corresponding help pages for details)

Examples

Run this code

  
  #Simplified yeast microarray data
  if (FALSE) { 
  data(BicatYeast)
  set.seed(1)
  bics1 <- biclust(BicatYeast,BCPlaid(), back.fit = 2, shuffle = 3, fit.model = ~m + a + b,
  row.release = 0.7, col.release = 0.7,
  verbose = FALSE, max.layers = 10, iter.startup = 5,
  iter.layer = 30)
  bubbleplot(BicatYeast,bics1, showLabels=TRUE)

  loma=binarize(BicatYeast,2)
  bics2=biclust(loma,BCBimax(), minr=4, minc=4, number=10)
  bubbleplot(BicatYeast,bics1,bics2)
  }