| mbrPlotDuals {RTNduals} | R Documentation |
This function plots the shared targets for a regulon pair.
mbrPlotDuals(
object,
dualreg,
filepath = NULL,
cols = c("#006400FF", "#CD6600FF")
)
object |
A processed object of class MBR evaluated by
the method |
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. |
A plot showing targets of dual regulons.
##--- 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)