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Last data update: 2014.03.03

R: Overlap of ISA biclusters

overlap

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)
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(eisa)
Loading required package: isa2
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/eisa/overlap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: overlap
> ### Title: Overlap of ISA biclusters
> ### Aliases: overlap overlapPlot
> ### Keywords: cluster
> 
> ### ** Examples
> 
> data(ALLModulesSmall)
> G <- overlap(ALLModulesSmall, algorithm="drl", edge.limit=0.3)

Attaching package: 'igraph'

The following objects are masked from 'package:IRanges':

    simplify, union

The following objects are masked from 'package:S4Vectors':

    compare, union

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> #if (interactive()) {
>   overlapPlot(G)
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>