overlap {eisa} | R Documentation

## Overlap of ISA biclusters

### Description

Plots a network, where each node is a module and modules that overlap are closer to each other.

### Usage

    overlap (modules, algorithm = c("mds", "fr", "drl"), edge.limit = 0.5)
    overlapPlot (graph, xsize = 400, ysize = 400, vertex.size = 20,
         vertex.size2 = 10, ...)

### Arguments

`modules` | An `ISAModules` object.
`algorithm` | The algorithm to use for placing the vertices, a character scalar. See details below.
`edge.limit` | Numeric constant between zero and one, only edges between modules that have a Pearson correlation higher than `edge.limit` will be drawn.
`graph` | An `igraph` object, as returned by `overlap`.
`xsize` | The width of the plot in pixels, only used to calculate the return value, it does not influence the plot itself.
`ysize` | The height of the plot in pixels, only used to calculate the return value, it does not influence the plot itself.
`vertex.size` | The width of the vertices on the plot.
`vertex.size2` | The height of the vertices on the plot.
`...` | Additional arguments, these are passed to the `plot.igraph` function from the `igraph` package.

### Details

An `ISAModules` object may potentially contain many modules that overlap. These functions visualize the overlapping relationships of a set of modules.

`overlap` creates an `igraph` graph with additional information on how to plot this graph in a way that nodes representing overlapping modules are close to each other.

`overlapPlot` takes such a graph and plots it.

`overlap` can use various algorithms, depending on the `algorithm` argument. If it is ‘`mds`’, then multi-dimensional scaling is used, by calling the `isaMDS` function in the `MASS` package. If it is ‘`fr`’, then the Fruchterman-Reingold algorithm is used, through the `layout.fruchterman.reingold` function of the `igraph` package. If it is ‘`drl`’, then the DrL graph layout algorithm is used, see the `layout.drl` function in the `igraph0` package.

### Value

`overlap` returns an igraph graph.

`overlapPlot` returns the coordinates of the vertices in a two-column matrix, invisibly.

### Author(s)

Gabor Csardi csardi.gabor@gmail.com

### References

Bergmann S, Ihmels J, Barkai N: Iterative signature algorithm for the analysis of large-scale gene expression data Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.

### Examples

    data(ALLModulesSmall)
    G <- overlap(ALLModulesSmall, algorithm="drl", edge.limit=0.3)
    if (interactive()) {
      overlapPlot(G)
    }

[Package eisa version 1.39.0 Index]