IntegratedJM (version 1.6)

volcano: volcano

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.

Value

A plot which looks like a volcano.

Details

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

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)")
# }