quantable (version 0.3.6)

volcano2G: DEPRECATED Volcano plot using ggplot and ggrepel

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

# NOT RUN {
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)

# }