parallelCoordinates: Parallel Coordinates

In biclust: BiCluster Algorithms

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)

Example output

Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
Loading required package: lattice
layer: 0 
 420.4547
layer: 1 
[1]  0 10 10
[1] 30 10 10
[1] 31 10 10
[1] 60 10 10
[1] 1
[1] 465.6663   0.0000   0.0000   0.0000
back fitting 2 times
layer: 2 
[1]  0 42 24
[1]  1 41 22
[1] 30 41 22
[1] 31  0 22
[1] 32
[1] 0 0 0 0
     
Layer Rows Cols  Df     SS    MS Convergence Rows Released Cols Released
    0  100   50 149 158.04  1.06          NA            NA            NA
    1   10   10  19 857.68 45.14           1             0             0

biclust documentation built on May 2, 2019, 5:56 p.m.