mbrPlotDuals: Plot shared targets between regulons.

In RTNduals: Analysis of co-regulation and inference of 'dual 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("tniData", package = "RTN")
gexp <- tniData$expData
annot <- tniData$rowAnnotation
tfs <- c("IRF8","IRF1","PRDM1","E2F3","STAT4","LMO4","ZNF552")

##--- 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)

RTNduals documentation built on Nov. 12, 2020, 2:03 a.m.