R: Parallel Coordinates

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

### See Also

`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 2.0.2 Index]