mbrPlotDuals: Plot shared target clouds between dual regulons.

In chagasVinicius/RTNmotifs: analysis of co-regulatory network motifs and inference of 'dual regulons'.

Description

This function plots the shared target clouds between a regulon pair.

Usage

mbrPlotDuals(object, names.motifs = NULL, filepath = NULL, alpha = 0.8,
  lncols = c("darkgreen", "darkorange3"), lwd = 0.7,
  estimator = "spearman")

Arguments

object	A processed object of class MBR evaluated by the method mbrAssociation.
names.motifs	A vector with 'dual regulon' indentifiers from the 'motifsInformation' table.
filepath	A character string indicating the file path where the plot should be saved.
alpha	The alpha transparency, a number in [0,1].
lncols	A vector of length 2 indicating the colors of the negative and positive target clouds, respectively.
lwd	Line width, a decimal value (between 0 and 1).
estimator	A character string indicating the association metric. One of "spearman" (default), "kendall", or "pearson", can be abbreviated.

Value

A plot with the shared target clouds between dual regulons.

Examples

data("dt4rtn", package = "RTN")
gexp <- dt4rtn$gexp
annot <- dt4rtn$gexpIDs
tfs1 <- dt4rtn$tfs[c("IRF8","IRF1","PRDM1","AFF3","E2F3")]
tfs2 <- dt4rtn$tfs[c("HCLS1","STAT4","STAT1","LMO4","ZNF552")]
##---mbrPreprocess
rmbr <- mbrPreprocess(gexp=gexp, regulatoryElements1 = tfs1, 
regulatoryElements2=tfs2, gexpIDs=annot)
##---mbrPermutation
rmbr <- mbrPermutation(rmbr, nPermutations=10)
##---mbrBootstrap
rmbr <- mbrBootstrap(rmbr, nBootstrap=10)
##---mbrDpiFilter
rmbr <- mbrDpiFilter(rmbr)
##---mbrAssociation
rmbr <- mbrAssociation(rmbr, prob=0.75)
##---mbrDuals
rmbr <- mbrDuals(rmbr)
##---
dual <- mbrGet(rmbr, what="dualRegulons")[1]
mbrPlotDuals(rmbr, names.motifs=dual)

chagasVinicius/RTNmotifs documentation built on May 13, 2019, 3:10 p.m.