viewPAN: Show posterior association networks or modules in 'igraph' or...

In PANR: Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

Description

The function display inferred posterior association networks or enriched functional gene modules in igraph or a powerful graphical visualization software RedeR.

Usage

viewPAN(object, what="graph", moduleID=1,
layout="layout.fruchterman.reingold", verbose=TRUE, ...)

Arguments

object	an object of S4 class PAN.
what	a character value specifying which to show: 'graph' or 'pvclustModule'.
moduleID	a numeric or integer vector of modules to view (see details in sigModules). This argument will be applied only when what=‘pvclustModule’.
layout	a character value specifying the layout method (see details in layout). This argument will be applied only when engine=‘igraph’ when build a graph for PAN using buildPAN.
verbose	a logical value to switch on (if TRUE) or off if FALSE detailed run-time message.
...	not in use, but only for further extension.

Details

This function presents the inferred posterior association network or enriched functional modules in igraph or RedeR depending on the graphics engine used when building the graph for PAN (details in buildPAN).

Please note that when viewing a dense PAN in ‘igraph’, it could be very messy. Multiple modules can be viewed at the same time in ‘RedeR’ powered by its feature of ‘containers’, which are used to group gene modules. When view multiple modules in ‘igraph’,

Author(s)

Xin Wang [e-mail]

References

Xin Wang, Mauro Castro, Klaas W. Mulder and Florian Markowetz, Posterior association networks and enriched functional gene modules inferred from rich phenotypic perturbation screens, in preparation.

See Also

buildPAN, layout

Examples

## Not run: 
data(bm, package="PANR")
pan<-new("PAN", bm1=bm1)
pan<-infer(pan, para=list(type="SNR", log=TRUE, sign=TRUE, cutoff=log(5)),
filter=FALSE, verbose=TRUE)
data(Bakal2007Cluster, package="PANR")
pan<-buildPAN(pan, engine="igraph", para=list(nodeColor=nodeColor, 
hideNeg=TRUE), verbose=TRUE)
##view inferred PAN
viewPAN(pan, what='graph', layout="layout.fruchterman.reingold")	

## End(Not run)

PANR documentation built on Nov. 8, 2020, 8:15 p.m.