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 Index]