TCGAvisualize_starburst: Create starburst plot

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Create starburst plot

Description

Create Starburst plot for comparison of DNA methylation and gene expression. The log10 (FDR-corrected P value) is plotted for beta value for DNA methylation (x axis) and gene expression (y axis) for each gene.

The black dashed line shows the FDR-adjusted P value of 0.01.

You can set names to TRUE to get the names of the significant genes.

Candidate biologically significant genes will be circled in the plot.

Candidate biologically significant are the genes that respect the expression (logFC.cut), DNA methylation (diffmean.cut) and significance thresholds (exp.p.cut, met.p.cut)

Usage

TCGAvisualize_starburst(
  met,
  exp,
  group1 = NULL,
  group2 = NULL,
  exp.p.cut = 0.01,
  met.p.cut = 0.01,
  diffmean.cut = 0,
  logFC.cut = 0,
  met.platform = c("Illumina Human Methylation 450", "Illumina Human Methylation 27",
    "Illumina Methylation Epic"),
  genome,
  names = FALSE,
  names.fill = TRUE,
  filename = "starburst.png",
  return.plot = FALSE,
  ylab = expression(atop("Gene Expression", paste(-Log[10],
    " (FDR corrected P values)"))),
  xlab = expression(atop("DNA Methylation", paste(-Log[10],
    " (FDR corrected P values)"))),
  title = "Starburst Plot",
  legend = "DNA Methylation/Expression Relation",
  color = NULL,
  label = c("Not Significant", "Up regulated & Hypo methylated",
    "Down regulated & Hypo methylated", "hypo methylated", "hyper methylated",
    "Up regulated", "Down regulated", "Up regulated & Hyper methylated",
    "Down regulated & Hyper methylated"),
  xlim = NULL,
  ylim = NULL,
  height = 10,
  width = 20,
  dpi = 600
)

Arguments

met	A SummarizedExperiment with methylation data obtained from the TCGAPrepare or Data frame from DMR_results file. Expected colData columns: diffmean, p.value.adj and p.value Execute volcanoPlot function in order to obtain these values for the object.
exp	Object obtained by DEArnaSEQ function
group1	The name of the group 1 Obs: Column p.value.adj.group1.group2 should exist
group2	The name of the group 2. Obs: Column p.value.adj.group1.group2 should exist
exp.p.cut	expression p value cut-off
met.p.cut	methylation p value cut-off
diffmean.cut	If set, the probes with diffmean higher than methylation cut-off will be highlighted in the plot. And the data frame return will be subseted.
logFC.cut	If set, the probes with expression fold change higher than methylation cut-off will be highlighted in the plot. And the data frame return will be subseted.
met.platform	DNA methylation platform "Illumina Human Methylation 450", "Illumina Human Methylation 27", "Illumina Methylation Epic"
genome	Genome of reference ("hg38" or "hg19") used to identify nearest probes TSS
names	Add the names of the significant genes? Default: FALSE
names.fill	Names should be filled in a color box? Default: TRUE
filename	The filename of the file (it can be pdf, svg, png, etc)
return.plot	If true only plot object will be returned (pdf will not be created)
ylab	y axis text
xlab	x axis text
title	main title
legend	legend title
color	vector of colors to be used in graph
label	vector of labels to be used in graph
xlim	x limits to cut image
ylim	y limits to cut image
height	Figure height
width	Figure width
dpi	Figure dpi

Details

Input: data with gene expression/methylation expression Output: starburst plot

Value

Save a starburst plot

Examples

## Not run: 
library(SummarizedExperiment)
met <- TCGAbiolinks:::getMetPlatInfo(
   genome = "hg38",
   platform = "Illumina Human Methylation 27"
 )
values(met) <- NULL
met$probeID <- names(met)
nrows <- length(met); ncols <- 20
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
colData <- S4Vectors::DataFrame(
  Treatment = rep(c("ChIP", "Input"), 5),
  row.names = LETTERS[1:20],
  group = rep(c("group1","group2"),c(10,10))
)
met <- SummarizedExperiment::SummarizedExperiment(
         assays = S4Vectors::SimpleList(counts=counts),
         rowRanges = met,
         colData = colData
)
rowRanges(met)$diffmean.g1.g2 <- c(runif(nrows, -0.1, 0.1))
rowRanges(met)$diffmean.g2.g1 <- -1*(rowRanges(met)$diffmean.g1.g2)
rowRanges(met)$p.value.g1.g2 <- c(runif(nrows, 0, 1))
rowRanges(met)$p.value.adj.g1.g2 <- c(runif(nrows, 0, 1))
exp <- TCGAbiolinks:::get.GRCh.bioMart("hg38")
exp$logFC <- runif(nrow(exp), -5, 5)
exp$FDR <- runif(nrow(exp), 0.01, 1)

result <- TCGAvisualize_starburst(
  met,
  exp,
  exp.p.cut = 0.05,
  met.p.cut = 0.05,
  logFC.cut = 2,
  group1 = "g1",
  group2 = "g2",
  genome = "hg38",
  met.platform = "27k",
  diffmean.cut = 0.0,
  names  = TRUE
)

## End(Not run)

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.