apComplex (version 2.38.0)

plotComplex: Render complex estimates

Description

plotComplex renders complex estimates from the apComplex algorithm using Rgraphviz.

Usage

plotComplex(complexMembers,g,VBs,VPs,geneName=FALSE,baitColor="yellow",preyColor="white",recipLineColor="red",unrecipBBLineColor="blue",unrecipBPLineColor="gray",y="neato")

Arguments

complexMembers

A character vector of proteins composing a complex estimate.

g

An object of class graph, the full bait-prey graph of AP-MS data used in analysis. complexMembers must be a subset of the node names of g.

VBs

A vector of viable baits used in the AP-MS experiment.

VPs

A vector of viable prey used in the AP-MS experiment.

geneName

A logical indicating whether or not nodes should be plotted with common gene names as labels rather than systematic names.

baitColor

Color of bait nodes.

preyColor

Color of prey nodes.

recipLineColor

Color of edges connecting baits which both detected each other as prey

unrecipBBLineColor

Color of edges connecting baits in which one bait finds the other as prey but not vice versa.

unrecipBPLineColor

Color of edges extending from baits to proteins that were only used as prey, hence reciprocity is not possible.

y

Layout of plot

Value

A plotted graph of the complex estimate subgraph.

Details

This is a simple function for plotting complex estimates resulting from the apComplex algorithm. Giving the upcoming changes in Rgraphviz, it will likely be changed substantially.

References

Scholtens D and Gentleman R. Making sense of high-throughput protein-protein interaction data. Statistical Applications in Genetics and Molecular Biology 3, Article 39 (2004).

Scholtens D, Vidal M, and Gentleman R. Local modeling of global interactome networks. Bioinformatics 21, 3548-3557 (2005).

See Also

findComplexes

Examples

data(apEX)
data(apEXG)
PCMG2 <- findComplexes(apEX,sensitivity=.7,specificity=.75)
PCMG2sorted <- sortComplexes(PCMG2,apEX)

VBs <- rownames(apEX)
VPs <- setdiff(colnames(apEX),VBs)

plotComplex(PCMG2sorted$MBME[[1]],g=apEXG,VBs=VBs, VPs=VPs)