parallelCoordinates {biclust}

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 [e-mail]

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)