plotCombinedPDF {qusage} | R Documentation |
A function for plotting out the pdfs for an indivdiual pathway in the QScomb object.
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", ...)
QScomb |
|
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.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 |
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.
##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")