ELMER (version 1.4.2)

TF.rank.plot: TF.rank.plot to plot the scores (-log10(P value)) which assess the correlation between TF expression and average DNA methylation at motif sites.

Description

TF.rank.plot is a function to plot the scores (-log10(P value)) which assess the correlation between TF expression and average DNA methylation at motif sites. The the motif relevant TF and top3 TFs will be labeled in a different color.

Usage

TF.rank.plot(motif.pvalue, motif, TF.label, dir.out = "./", save = TRUE)

Arguments

motif.pvalue

A matrix or a path specifying location of "XXX.with.motif.pvalue.rda" which is output of get.TFs.

motif

A vector of charactors specify the motif to plot

TF.label

A list shows the labels for each motif. If TF.label is not specified, the motif relevant TF and top3 TF will be labeled.

dir.out

A path specify the directory to which the figures will be saved. Current directory is default.

save

A logic. If true (default), figure will be saved to dir.out.

Value

A plot shows the score (-log(P value)) of association between TF expression and DNA methylation at sites of a certain motif.

Examples

load(system.file("extdata","getTF.hypo.TFs.with.motif.pvalue.rda",package="ELMER"))
TF.rank.plot(motif.pvalue=TF.meth.cor, motif="TP53", TF.label=list(TP53=c("TP53","TP63","TP73")),
            save=FALSE)