plotCombinedPDF {qusage} | R Documentation

## Plot combined PDF for an individual pathway

### 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")

[Package qusage version 2.20.0 Index]