TCGAbiolinks (version 1.2.5)

TCGAvisualize_starburst: 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, names = FALSE, names.fill = TRUE, circle = TRUE, filename = "starburst.pdf", 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.

names

Add the names of the significant genes? Default: FALSE

names.fill

Names should be filled in a color box? Default: TRUE

circle

Circle pair gene/probe that respects diffmean.cut and logFC.cut 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

Value

Save a starburst plot

Details

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

Examples

nrows <- 20000; ncols <- 20
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
ranges <- GenomicRanges::GRanges(rep(c("chr1", "chr2"), c(5000, 15000)),
                   IRanges::IRanges(floor(runif(20000, 1e5, 1e6)), width=100),
                    strand=sample(c("+", "-"), 20000, TRUE),
                    probeID=sprintf("ID%03d", 1:20000),
                    Gene_Symbol=sprintf("ID%03d", 1:20000))
colData <- S4Vectors::DataFrame(Treatment=rep(c("ChIP", "Input"), 5),
                    row.names=LETTERS[1:20],
                    group=rep(c("group1","group2"),c(10,10)))
data <- SummarizedExperiment::SummarizedExperiment(
         assays=S4Vectors::SimpleList(counts=counts),
         rowRanges=ranges,
         colData=colData)
met <- data
exp <- data.frame(row.names=sprintf("ID%03d", 1:20000),
                  logFC=runif(20000, -5, 5),
                  FDR=runif(20000, 0.01, 1))
SummarizedExperiment::rowRanges(met)$diffmean.g1.g2 <- c(runif(20000, -0.1, 0.1))
SummarizedExperiment::rowRanges(met)$diffmean.g2.g1 <- -1*(SummarizedExperiment::rowRanges(met)$diffmean.g1.g2)
SummarizedExperiment::rowRanges(met)$p.value.g1.g2 <- c(runif(20000, 0, 1))
SummarizedExperiment::rowRanges(met)$p.value.adj.g1.g2 <- c(runif(20000, 0, 1))
result <- TCGAvisualize_starburst(met,exp,
                                  exp.p.cut = 0.05, met.p.cut = 0.05,
                                  group1="g1",group2="g2",
                                  diffmean.cut=0.0,
                                  names=TRUE, circle = FALSE)
result <- TCGAvisualize_starburst(SummarizedExperiment::values(met),
                                  exp,
                                  exp.p.cut = 0.05, met.p.cut = 0.05,
                                  group1="g1",group2="g2",
                                  diffmean.cut=0.0,
                                  names=TRUE, circle = FALSE)