parallelCoordinates {biclust} R Documentation

## Parallel Coordinates

### Description

Represents expression levels through gene and/or condition profiles in a bicluster as lines.

### Usage

parallelCoordinates(x, bicResult, number, plotBoth = FALSE, plotcol = TRUE,
compare = TRUE, info = F, bothlab = c("Rows", "Columns"), order = FALSE,
order2 = 0,ylab = "Value" , col=1,...)


### Arguments

 x The data matrix of the bicluster to be drawn bicResult BiclustResult object with a bicluster result set number Bicluster to be drawn from the result set 'bicResult' plotBoth If 'TRUE', Parallel Coordinates of rows (Genes) and columns (Conditions) were drawn one below the other. plotcol If 'TRUE', columns profiles are drawn, so each line represents one of the columns in the bicluster. Otherwise, row profiles are drawn. Default 'TRUE' compare If 'TRUE', values of the complete data matrix are considered and drawn as shaded lines. Default 'TRUE' info If 'TRUE', a prepared Title is drawn bothlab Names of the x Axis if PlotBoth order Rows and/or Columns are in increasing order. order2 Which ordering. ylab ylab col col ... Plot Parameters

### Author(s)

Rodrigo Santamaria, Martin Sill and Sebastian Kaiser sebastian.kaiser@stat.uni-muenchen.de

drawHeatmap for alternative representation of biclusters and bubbleplot for simultaneous representation of biclusters.

### 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)
parallelCoordinates(x=s2,bicResult=bics,number=1, plotBoth=TRUE,
plotcol=TRUE, compare=TRUE, info=TRUE,bothlab=c("Genes Bicluster
1","Conditions Bicluster 1"), order =TRUE)
parallelCoordinates(x=s2,bicResult=bics,number=1, plotBoth=FALSE, plotcol=TRUE,
compare=FALSE, info=TRUE)


[Package biclust version 2.0.3.1 Index]