plot3dModule: 3D plot of the network

In assaron/BioNet: Routines for the functional analysis of biological networks

Description

The function plots a network from graphNEL or igraph format in 3D using a modified function from the package igraph and requires the package rgl which uses openGL. The 3D plot can be zoomed, rotated, shifted on the canvas. This function is just used to visualize the modules. For further plotting options use the rglplot function of the igraph package. If a score attribute is provided in the graph this will be used for the coloring of the nodes. Otherwise a vector of values can be given by the diff.or.score argument. The vector has to contain positive and negative values, either scores or values for differential expression (fold changes). Labels for the nodes can be provided by the labels argument, otherwise it will be automatically looked for a geneSymbol attribute of the nodes.

Usage

plot3dModule(network, labels=NULL, windowSize = c(100,100,1500,1000), diff.or.scores=NULL, red=c("negative", "positive"), ...)

Arguments

network	Network in graphNEL or igraph format.
labels	Labels for the nodes of the network. Otherwise it will be automatically looked for a geneSymbol attribute of the nodes.
windowSize	Numerical vector of size four to set the size of the rgl device.
diff.or.scores	Named numerical vector of differential expression (fold changes) or scores of the nodes in the network. These will be used for node coloring. Otherwise a score attribute of the nodes will be automatically used.
red	Either "negative" or "positive", to specify which values are to be colored red in the plot.
...	Other graphic parameters for the plot.

Author(s)

Daniela Beisser

See Also

save3dModule, plotModule

Examples

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

## Not run: library(rgl);
plot3dModule(network=subnet, diff.or.score=diff)
## End(Not run)

assaron/BioNet documentation built on Sept. 18, 2020, 12:02 a.m.