TF.rank.plot: TF.rank.plot to plot the scores (-log10(P value)) which...

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

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,
  title = NULL,
  TF.label = NULL,
  dir.out = "./",
  save = TRUE,
  cores = 1
)

Arguments

motif.pvalue	A matrix or a path specifying location of "XXX.with.motif.pvalue.rda" which is output of getTF.
motif	A vector of characters specify the motif to plot
title	Tite title (the motif will still be added to the title)
TF.label	A list shows the label 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
cores	A interger which defines the number of cores to be used in parallel process. Default is 1: no parallel process.

Value

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

Author(s)

Lijing Yao (maintainer: [e-mail])

Examples

library(ELMER)
data <- tryCatch(ELMER:::getdata("elmer.data.example"), error = function(e) {
  message(e)
  data(elmer.data.example, envir = environment())
})
enriched.motif <- list("P53_HUMAN.H11MO.0.A"= c("cg00329272", "cg10097755", "cg08928189",
                                 "cg17153775", "cg21156590", "cg19749688", "cg12590404",
                                 "cg24517858", "cg00329272", "cg09010107", "cg15386853",
                                 "cg10097755", "cg09247779", "cg09181054"))
TF <- get.TFs(data, 
              enriched.motif, 
              group.col = "definition",
              group1 = "Primary solid Tumor", 
              group2 = "Solid Tissue Normal",
              TFs = data.frame(
                     external_gene_name=c("TP53","TP63","TP73"),
                     ensembl_gene_id= c("ENSG00000141510",
                                        "ENSG00000073282",
                                        "ENSG00000078900"),
                     stringsAsFactors = FALSE),
             label="hypo")
TF.meth.cor <- get(load("getTF.hypo.TFs.with.motif.pvalue.rda"))            
TF.rank.plot(motif.pvalue=TF.meth.cor,  
            motif="P53_HUMAN.H11MO.0.A", 
            TF.label=createMotifRelevantTfs("subfamily")["P53_HUMAN.H11MO.0.A"],
            save=TRUE)
TF.rank.plot(motif.pvalue=TF.meth.cor,  
            motif="P53_HUMAN.H11MO.0.A", 
            save=TRUE)
# Same as above
TF.rank.plot(motif.pvalue=TF.meth.cor,  
            motif="P53_HUMAN.H11MO.0.A", 
            dir.out = "TFplots",
            TF.label=createMotifRelevantTfs("family")["P53_HUMAN.H11MO.0.A"],
            save=TRUE)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.