TCGAVisualize_volcano: Creates a volcano plot for DNA methylation or expression

Description Usage Arguments Details Value Examples

Description

Creates a volcano plot from the expression and methylation analysis.

Usage

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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

y

y-axis data

filename

Filename. Default: volcano.pdf, volcano.svg, volcano.png

ylab

y axis text

xlab

x axis text

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

ylim

y limits to cut image

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

p-values threshold.

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 expression and methylation analysis. Please see the vignette for more information Observation: This function automatically is called by TCGAanalyse_DMR

Value

Saves the volcano plot in the current folder

Examples

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x <- runif(200, -1, 1)
y <- runif(200, 0.01, 1)
TCGAVisualize_volcano(x,y)
## Not run: 
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()}

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.