monsterdTFIPlot: This function plots the Off diagonal mass of an observed...

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

This function plots the Off diagonal mass of an observed Transition Matrix compared to a set of null TMs

Description

This function plots the Off diagonal mass of an observed Transition Matrix compared to a set of null TMs

Usage

monsterdTFIPlot(
  monsterObj,
  rescale = "none",
  plot.title = NA,
  highlight.tfs = NA,
  nTFs = -1
)

Arguments

monsterObj	monsterAnalysis Object
rescale	string indicating whether to reorder transcription factors according to their statistical significance and to rescale the values observed to be standardized by the null distribution ('significance'), to reorder transcription factors according to the largest dTFIs ('magnitude') with the TF x axis labels proportional to their significance , or finally without ordering them ('none'). When rescale is set to 'significance', the results can be different between two MONSTER runs if the number of permutations is not large enough to sample the null, that is why it is the seed should be set prior to calling MONSTER to get reproducible results. If rescale is set to another value such as 'magnitude' or 'none', it will produce deterministic results between two identical MONSTER runs.
plot.title	String specifying the plot title
highlight.tfs	vector specifying a set of transcription factors to highlight in the plot
nTFs	number of TFs to plot in x axis. -1 takes all TFs.

Value

ggplot2 object for transition matrix comparing observed distribution to that estimated under the null

Examples

# data(yeast)
# yeast$exp.cc[is.na(yeast$exp.cc)] <- mean(as.matrix(yeast$exp.cc),na.rm=TRUE)
# design <- c(rep(0,20),rep(NA,10),rep(1,20))
# monsterRes <- monster(yeast$exp.cc, design, yeast$motif, nullPerms=100, numMaxCores=4)#' 
data(monsterRes)
monsterdTFIPlot(monsterRes)

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.