Volcano: Create a Volcano plot

In BenaroyaResearch/DGETools: Differential Gene Expression Tools

Create a Volcano plot

Description

Make a volcano plot, using cuts, ggrepel, optionally write out as image, optionally write out DEG list and all gene list to .csv

Usage

Volcano(
  fit,
  target,
  title,
  numLabels = 50,
  write = FALSE,
  writeTopTable = FALSE,
  saveImage = FALSE,
  imageWidth = 8,
  imageHeight = 10,
  ext = "png",
  extImage = "png",
  cutFC = 1.5,
  cutPvalue = 0.05,
  labelList = NULL,
  labelSize = 4,
  labelSource = "hgnc_symbol",
  colors = c("red", "blue", "grey"),
  legendStrings = c("Up regulated", "Down regulated", "Not significant"),
  repelFontFace = theme_get()$text$face,
  repelSize = 4,
  pointSize = 3,
  annLocation = "bottom",
  leftAnnText = NULL,
  rightAnnText = NULL,
  ...
)

Arguments

fit	A fitted linear model object from limma/eBayes (MArrayLM), or a data frame with slots like the result of topTable
target	Name of the contrast target to plot, or the corresponding column of the model matrix (string)
title	Title for the plot (string)
numLabels	Number of labels to print (integer)
write	deprecated in favor of writeTopTable
writeTopTable	Write gene list to CSV file (see target string, boolean)
saveImage	Write out an image (boolean)
imageWidth	Width of saved image in inches (floating point)
imageHeight	Height of saved image in inches (floating point)
ext	deprecated in favor of extImage
extImage	Image type/extension (string)
cutFC	Fold Change cutoff for significance (floating point)
cutPvalue	p-valut cutoff for significance (floating point)
labelList	List of label names to render, only those (vector)
labelSize	Size of text in repel for labels from labelList - default is the same as the repelSize (integer)
labelSource	Name of the column for gene names (string)
colors	vector of up/right point color, down/left point color, and not significant color (vector of three strings)
legendStrings	vector of up, down, not significant (vector of strings)
repelFontFace	Name of fontface for labels (string)
repelSize	Size of text repel labels (integer)
pointSize	Size of geom_points (integer)
annLocation	Location of side annotations (string)
leftAnnText	Text for the left side annotation (string)
rightAnnText	Text for the right side annotation (string)
...	Additional function calls from the ggplot2 package to be added to ggplot, such as xlim=xlim(-5,5), ylim=ylim(0,9)

Value

A dataframe of differentially expressed gene information, in the form of topTable().

Author(s)

Scott R Presnell, [e-mail]

See Also

Associated or similar limma functions topTable, volcanoplot

Examples

Volcano(fit, "SPvsDP", "Single Positive vs Double Positive")

BenaroyaResearch/DGETools documentation built on July 2, 2022, 12:19 p.m.