mbrPlotDuals {RTNduals}R Documentation

Plot shared targets between regulons.

Description

This function plots the shared targets for a regulon pair.

Usage

mbrPlotDuals(object, dualreg, filepath = NULL, cols = c("#006400FF",
  "#CD6600FF"))

Arguments

object

A processed object of class MBR evaluated by the method mbrAssociation.

dualreg

A string indicating the name of a dual regulon.

filepath

A string indicating the file path where the plot should be saved.

cols

A vector of length 2 indicating a diverging color scheme for negative and positive correlations, respectively.

Value

A plot showing targets of dual regulons.

Examples


##--- load a dataset for demonstration
data("dt4rtn", package = "RTN")
gexp <- dt4rtn$gexp
annot <- dt4rtn$gexpIDs
tfs <- dt4rtn$tfs[c("IRF8","IRF1","PRDM1","AFF3","E2F3")]

##--- construct a tni object
rtni <- tni.constructor(gexp, regulatoryElements = tfs, rowAnnotation=annot)

##--- compute regulons 
## set nPermutations>=1000
rtni <- tni.permutation(rtni, nPermutations=30)
## set nBootstrap>=100
rtni <- tni.bootstrap(rtni, nBootstrap=30)
## 'eps=NA' estimates threshold from empirical null
rtni <- tni.dpi.filter(rtni, eps=NA)

##--- construct a mbr object
rmbr <- tni2mbrPreprocess(rtni)

##--- run mbrAssociation 
## set nPermutations>=1000
rmbr <- mbrAssociation(rmbr, pValueCutoff = 0.05, nPermutations=30)

## Not run: 

##--- get inferred duals and plot the shared cloud of targets
duals <- mbrGet(rmbr, what="dualRegulons")
mbrPlotDuals(rmbr, dualreg=duals[1])


## End(Not run)

[Package RTNduals version 1.6.2 Index]