qusage (version 2.4.0)

plotDensityCurves: Plot gene set PDFs

Description

A function for plotting out the pdfs of a set of pathways.

Usage

plotDensityCurves(QSarray, path.index=1:numPathways(QSarray), zeroLine=TRUE, addVIF=!is.null(QSarray$vif), col=NULL, plot=TRUE, add=FALSE, xlim=NULL,ylim=NULL, xlab=NULL,ylab=NULL, type="l", ...)

Arguments

QSarray

QSarray object

path.index

vector describing which pathways to plot. Can either be numeric or a character vector containing the names of the pathways to plot.

zeroLine

a logical indicating whether to include a vertical line at 0.

addVIF

a logical indicating whether the VIF should be used to calculate the variance of the pathway.

col

the color of the curves. Can be a vector of the same length as path.index specifying the color of each individual curve.

plot

Logical indicating whether to create the plot. If FALSE, only the coordinates for the plot will be returned, and no new plot will be created.

add, xlim, ylim, xlab, ylab, type, ...

parameters to be passed on to plot

Value

Invisibly returns a list of the same length as path.index, where each entry is a matrix of x- and y-coordinates for that pathway.

Details

This function uses the data produced by aggregateGeneSet to plot the PDFs of the pathways in QSarray. By default, plotDensityCurves will plot a curve for each pathway in the QSarray pathway, but this behavior can be controlled by the path.index parameter. For the best plots, it is suggested that you limit the number of curves plotted to below ten.

Examples

   ##create example data
  eset = matrix(rnorm(500*20),500,20, dimnames=list(1:500,1:20))
  labels = c(rep("A",10),rep("B",10))
    
  ##genes 1:30 are differentially expressed
  eset[1:30, labels=="B"] = eset[1:30, labels=="B"] + 1
  geneSets = list(diff.set=1:30, base.set=31:60)
  
  ##Run qusage
  set.results = qusage(eset, labels, "B-A", geneSets)
 
  ##Plot results
  plotDensityCurves(set.results)
  
  ##plot just the first curve with a different color
  plotDensityCurves(set.results, path.index=1, col=2, lwd=2)
  
  ##plot the CDFs of the curves
  coords = plotDensityCurves(set.results, plot=FALSE)
  plot(0, type="n", xlim=c(-1,2),ylim=c(0,1),xlab="x",ylab="CDF")
  for(i in 1:length(coords)){
    points = coords[[i]]
    x = points$x
    y = cumsum(points$y)/sum(points$y)
    lines(x,y,col=i)
  }