volcano2GB: Volcano with more control

In wolski/quantable: Streamline Descriptive Analysis of Quantitative Data Matrices

Description

Volcano with more control

Usage

volcano2GB(dataX, foldchange = "log2FC", pvalue = "q.mod",
  labels = "names", pthresh = 0.1, log2FCThresh = 0.5, main = NULL,
  xlab = "log2 FC", ylab = "-log10(Q Value)", repel.text.size = 1,
  repel.segment.size = 0.5, repel.segement.alpha = 0.5,
  pseudo = NULL, maxNrOfSignificantText = 20)

Arguments

dataX	dataX frame
foldchange	column name with fold change plotted on X
pvalue	column with pvalue or qvalue plotted as -log10 on y axes
labels	column containing lables
pthresh	horizontal abline
log2FCThresh	vertical abline
main	main plot title
xlab	xlab
ylab	ylab
repel.text.size	ggrepel parameter
repel.segment.size	ggrepel parameter
repel.segement.alpha	ggrepel parameter
pseudo	add pseudo fold changes
maxNrOfSignificantText	numeric - how many text labels to display - default = 20.

Examples

rm(list=ls())
library(tidyverse)
library(ggrepel)
library(quantable)
foldchange <- rnorm(1000)
pvals <-rexp(1000)
names <- sample(colors(),1000,replace=TRUE)

dataX <- data.frame(q.mod = pvals,
 log2FC = foldchange,
  names = names )
colnames(dataX)
b <- volcano2GB(dataX, pthresh=0.1, log2FCThresh=0.5 ,
main='test', repel.segment.size=0.3,repel.text.size=2)
b
dataX <- data.frame(a.q.mod = pvals,
 log2FC = foldchange,
  names = names )
b <- volcano2GB(dataX,
               pvalue = "a.q.mod",
               pthresh=0.1,
               log2FCThresh=0.5 ,
               main='test',
               repel.segment.size=0.3,
               repel.text.size=2)
b
b <- volcano2GB(dataX,
               pvalue = "a.q.mod",
               pthresh=0.1,
               log2FCThresh=0.5 ,
               main='test',
               repel.segment.size=0.3,
               repel.text.size=2,
               maxNrOfSignificantText=1000
               )
b

wolski/quantable documentation built on Nov. 26, 2021, 9:58 a.m.