plotModule: Plot of the network

In BioNet: Routines for the functional analysis of biological networks

Description

The function plots a network from graphNEL or igraph format, adapted from an igraph plotting function. It is just used to visualize the modules. For further plotting options use the plot.igraph function of the igraph package. The shapes of the nodes can be changed according to the scores argument, then negative scores appear squared. The color of the nodes can be changed according to the diff.expr argument. Negative values lead to green nodes, positive values are colored in red. If the vectors are not provided, it will be automatically looked for nodes attributes with the name score and diff.expr.

Usage

plotModule(network, layout=layout.fruchterman.reingold, labels=NULL, diff.expr=NULL, scores=NULL, main=NULL, vertex.size=NULL, ...)

Arguments

network	Network in graphNEL or igraph format.
layout	Layout algorithm, e.g. layout.fruchterman.reingold or layout.kamada.kawai.
labels	Labels for the nodes of the network.
diff.expr	Named numerical vector of differential expression (fold changes) of the nodes in the network. These will be used for coloring of the nodes. It will be automatically looked for nodes attribute with the name diff.expr, if the argument is null.
scores	Named numerical vector of scores of the nodes in the network. These will be used for the shape of the nodes. It will be automatically looked for nodes attribute with the name score, if the argument is null.
main	Main title of the plot.
vertex.size	Numerical value or verctor for the size of the vertices.
...	Other graphic parameters for the plot.

Author(s)

Marcus Dittrich and Daniela Beisser

See Also

plot3dModule

Examples

library(DLBCL)
data(dataLym)
data(interactome)
interactome <- subNetwork(dataLym$label, interactome)
interactome <- rmSelfLoops(interactome)
fchange <- dataLym$diff
names(fchange) <- dataLym$label
# create random subnetwork
subnet <- largestComp(subNetwork(nodes(interactome)[1:100], interactome))
fchange <- fchange[nodes(subnet)]

# color random subnetwork by the fold change
## Not run: plotModule(network=subnet, diff.expr=fchange)

Example output

Loading required package: graph
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, sd, var, xtabs

The following objects are masked from ‘package:base’:

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

Loading required package: RBGL
Loading required package: Biobase
Welcome to Bioconductor

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

BioNet documentation built on Nov. 8, 2020, 5:48 p.m.