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("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)