TCGAVisualize_volcano: Creates a volcano plot for DNA methylation or gene expression

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

Creates a volcano plot for DNA methylation or gene expression

Description

Creates a volcano plot from the gene expression and DNA methylation analysis.

Usage

TCGAVisualize_volcano(
  x,
  y,
  filename = "volcano.pdf",
  ylab = expression(paste(-Log[10], " (FDR corrected P-values)")),
  xlab = NULL,
  title = "Volcano plot",
  legend = NULL,
  label = NULL,
  xlim = NULL,
  ylim = NULL,
  color = c("black", "red", "green"),
  names = NULL,
  names.fill = TRUE,
  show.names = "significant",
  x.cut = 0,
  y.cut = 0.01,
  height = 5,
  width = 10,
  highlight = NULL,
  highlight.color = "orange",
  names.size = 4,
  dpi = 300
)

Arguments

x	x-axis data (i.e. Diff mean beta-values or Log2FC).
y	FDR adjusted p-value (q-value). This data will be transformed to -log10 values.
filename	File name: volcano.pdf, volcano.svg, volcano.png. If NULL returns the ggplot object.
ylab	y axis text. Default: -Log10 FDR corrected P-values
xlab	x axis text. Default: No text. Examples of input: expression(paste(Log[2], "FoldChange"))
title	main title. If not specified it will be "Volcano plot (group1 vs group2)
legend	Legend title
label	vector of labels to be used in the figure. Example: c("Not Significant","Hypermethylated in group1", "Hypomethylated in group1"))#'
xlim	x limits to cut image (i.e. c(-4,4))
ylim	y limits to cut image (i.e. c(-1,10))
color	vector of colors to be used in graph
names	Names to be plotted if significant. Should be the same size of x and y
names.fill	Names should be filled in a color box? Default: TRUE
show.names	What names will be showed? Possibilities: "both", "significant", "highlighted"
x.cut	x-axis threshold. Default: 0.0 If you give only one number (e.g. 0.2) the cut-offs will be -0.2 and 0.2. Or you can give different cut-offs as a vector (e.g. c(-0.3,0.4))
y.cut	q-values threshold (i.e. 0.01, 10^-10)
height	Figure height
width	Figure width
highlight	List of genes/probes to be highlighted. It should be in the names argument.
highlight.color	Color of the points highlighted
names.size	Size of the names text
dpi	Figure dpi

Details

Creates a volcano plot from the gene expression and DNA methylation analysis. Please see the vignette for more information

Value

Saves the volcano plot in the current folder

Examples

log2_foldchange <- runif(200, -2, 2)
fdr <- runif(200, 0.01, 1)
TCGAVisualize_volcano(
    x = log2_foldchange,
    y = fdr,
    x.cut = 1.5,
    y.cut = 0.01,
    title = "Title example",
    xlab = expression(paste(Log[2], "FoldChange"))
)
## Not run: 
beta_diff <- runif(200, -1, 1)
fdr <- runif(200, 0.01, 1)
TCGAVisualize_volcano(
    x = beta_diff,
    y = fdr,
    x.cut = 1.5,
    y.cut = 0.01,
    title = "Title example",
    xlab = expression(paste("DNA Methylation difference (", beta, "-values)"))
)
TCGAVisualize_volcano(
  x,
  y,
  filename = NULL,
  y.cut = 10000000,
  x.cut=0.8,
   names = rep("AAAA",length(x)),
   legend = "Status",
   names.fill = FALSE
)

TCGAVisualize_volcano(
  x,
  y,
  filename = NULL,
  y.cut = 10000000,
  x.cut = 0.8,
   names = as.character(1:length(x)),
   legend = "Status",
   names.fill = TRUE, highlight = c("1","2"),
   show = "both"
)
TCGAVisualize_volcano(
  x,
  y,
  filename = NULL,
  y.cut = 10000000,
  x.cut = c(-0.3,0.8),
  names = as.character(1:length(x)),
  legend = "Status",
  names.fill = TRUE,
  highlight = c("1","2"),
  show = "both"
)

## End(Not run)
while (!(is.null(dev.list()["RStudioGD"]))){dev.off()}

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