plotCombinedPDF: Plot combined PDF for an individual pathway

In arcolombo/junk: qusage: Quantitative Set Analysis for Gene Expression

Description

A function for plotting out the pdfs for an indivdiual pathway in the QScomb object.

Usage

plotCombinedPDF(QScomb,
                path.index=1,
                zeroLine=TRUE,
                comb.lwd=3,path.lwd=1,
                comb.col=par("col"),
                path.col=NULL,
                legend=FALSE,legend.labs=NULL,
                add=FALSE,
                xlim=NULL,ylim=NULL,
                xlab=NULL,ylab=NULL,
                main=NULL,
                type="l",
                ...)
 

Arguments

QScomb	QScomb object
path.index	index describing which pathway to plot. Can either be numeric or a string containing the names of the pathway to plot. Must be of length 1
zeroLine	a logical indicating whether to include a vertical line at 0.
comb.lwd	the lwd for the combined PDF curve.
path.lwd	the lwd for the individual dataset curves. Can be a vector of the same length as QScomb$QSlist specifying the lwd of each individual curve.
comb.col	the color of the combined PDF curve.
path.col	the color of the individual dataset curves. Can be a vector of the same length as QScomb$QSlist specifying the color of each individual curve.
legend	boolean; should a legend be added to the plot? Can also be a character vector specifying the location of the legend (i.e "topleft" vs "topright", etc. See legend for details)
legend.labs	character vector; the names of each dataset in QScomb$QSlist. If not provided, the function will attempt to pull the labels from QScomb$QSlist, or will use default names if those are undefined.
add, xlim, ylim, xlab, ylab, main, type, ...	parameters to be passed on to plot

Details

This function uses the data produced by combinePDFs to plot both the individual dataset PDFs and the combined PDF for a single pathway. By default, plotCombinedPDF will plot the PDFs for the first pathway in QScomb, but this behavior can be controlled by the path.index parameter.

Examples

  ##create 5 example datasets of different sizes
  esets = lapply(1:5, function(i){
    n = 20 + i*5
    eset = matrix(rnorm(500*n),500,n, dimnames=list(1:500,1:n))
    
    labels = c(rep("A",10+5*floor(i/2)),
               rep("B",10+5*ceiling(i/2))
              )
               
    ##genes 1:30 are differentially expressed
    eset[1:30, labels=="B"] = eset[1:30, labels=="B"] + rnorm(30,rnorm(1,0.5,0.5),1)
    
    return(list(eset=eset, labels=labels))
  })
    
  ##gene sets
  geneSets = list(diff.set=1:30, baseline.set=31:60)
  
  ##Run qusage on each dataset
  set.results = lapply(esets, function(dat){
    qusage(dat$eset, dat$labels, "B-A", geneSets)
  })
  
  ##run the combinePDFs function
  combined = combinePDFs(set.results)
  
  ##plot the combined PDF result for "diff.set"
  plotCombinedPDF(combined, path.index="diff.set")
  
 

arcolombo/junk documentation built on May 10, 2019, 12:49 p.m.