volcano2G: DEPRECATED Volcano plot using ggplot and ggrepel

In quantable: Streamline Descriptive Analysis of Quantitative Data Matrices

Description

DEPRECATED Volcano plot using ggplot and ggrepel

Usage

volcano2G(foldchange, pvals, labels, pthresh = 0.1, log2FCThresh = 0.5,
  main = NULL, xlab = "log2 FC", ylab = "-log10(Q Value)", xlim = c(-5,
  5), ylim = c(0, -log10(min(pvals, na.rm = TRUE))), size = 1,
  segment.size = 0.3, segement.alpha = 0.3, pseudo = NULL,
  colors = NULL)

Arguments

foldchange	vector with fold changes
pvals	vector with pvalues
labels	vector with labels
pthresh	pvalue threshold
log2FCThresh	log2 FC threshold
main	main title
xlab	xlab
ylab	ylab
xlim	xlim
ylim	ylim
size	see geom_text_repel
segment.size	see geom_text_repel
segement.alpha	see geom_text_repel
pseudo	usually q.mod containing NAs
colors	specify colors for specific lables.

Examples

rm(list=ls())
library(quantable)
foldchange <- rnorm(1000)
pvals <-rexp(1000)
volcano2G(foldchange, pvals,labels=rep("abcde", length(pvals)),
  pthresh=0.1, log2FCThresh=0.5,main='test',size=2,segment.size=0.3)

quantable documentation built on May 2, 2019, 4:05 p.m.