volcano: volcano

In IntegratedJM: Joint Modeling of the Gene-Expression and Bioassay Data, Taking Care of the Effect Due to a Fingerprint Feature

Description

The volcano function produces the volcano plot for logratio / fp-effect vs corresponding p-values.

Usage

volcano(x, pValue, pointLabels, topPValues = 10, topXvalues = 10,
  smoothScatter = TRUE, xlab = NULL, ylab = NULL, main = NULL,
  newpage = TRUE, additionalPointsToLabel = NULL,
  additionalLabelColor = "red", dir = TRUE)

Arguments

x	Numeric vector of logratios or covariate effect values to be plotted.
pValue	Numeric vector of corresponding p-values obtained from some statistical test.
pointLabels	Character vector providing the texts for the points to be labelled in the plot.
topPValues	Number of top p-values to be labelled. Default value is 10.
topXvalues	Number of top logratios or covariate effect values to be labelled. Default value is 10.
smoothScatter	Logical parameter to decide if a smooth plot is expected or not. Default is TRUE.
xlab	Text for the x-axis of the plot. Default is NULL.
ylab	Text for the y-axis of the plot. Default is NULL.
main	Text for the main title of the plot. Default is NULL.
newpage	Logical parameter
additionalPointsToLabel	Set of points other than the top values to be labelled in the plot. Default is NULL.
additionalLabelColor	Colour of the additionally labelled points. Default colour is red.
dir	Logical parameter deciding if the top values should be in decreasing (= TRUE) or increasing (= FALSE) order. Default is TRUE.

Details

Creates a plot which looks like a volcano with the interesting points labelled within the plot.

Value

A plot which looks like a volcano.

Examples

## Not run: 
volcano(x=jmRes$CovEffect1,pValue=jmRes$rawP1,pointLabels=rownames(jmRes),
topPValues = 10, topXvalues = 10,xlab="FP Effect (alpha)",ylab="-log(p-values)")

## End(Not run)

IntegratedJM documentation built on May 2, 2019, 6:47 p.m.