J.delasHeras at ed.ac.uk wrote: > Quoting "James W. MacDonald" <jmacdon at="" med.umich.edu="">: > >> J.delasHeras at ed.ac.uk wrote: >> >>> Quoting "D.Enrique ESCOBAR ESPINOZA" <escobarebio at="" yahoo.com="">: >>> >>> >>>> HI , >>>> does someone know if there is a built-inn >>>> function for adding a legend to the QC grph obtained >>>> with : >>>> data(Dilution) >>>> plot(qc(Dilution)) >>>> or if there is an easy way to add a legend to this graph >>>> thanks. >>> >>> >>> >>> In general I find that one or some of these functions help me >>> annotate any plot in R: >>> >>> ?text >>> ?mtext >>> ?title >>> ?legend >>> >>> I presume you probably were looking for 'legend'. >> >> >> Unfortunately legend won't work in this case. The qc() plot is produced >> after a call to layout(), which cuts the plotting device into four >> sections. The last section to be plotted is the upper left hand, which >> contains the names of the QC probesets. If you make a call to legend(), >> it will put the legend in that very small section, most likely right on >> top of the names of the QC probesets. >> >> To see what I mean, try this code (which comes directly from this >> plotting function): >> >> m <- matrix(c(4, 2, 1, 3), nrow = 2, ncol = 2) >> layout(m, c(1, 2), c(0.1, 1)) >> layout.show(4) >> >> The plots will be added to each box in the order listed. >> >> That said, if you want to hack the code it wouldn't be that difficult >> to add a call to legend() right after the second call to plot() in the >> function plot.qc.stats(). This will put a legend in the second layout >> box, which currently only contains the chip names on the extreme right >> edge. If you placed the legend "upperleft" and made the font size small >> enough, it might fit. >> >> Luckily, since simpleaffy doesn't use a namespace, you can simply >> copy-paste the function into an editor, hack away, then source() back >> in and go. >> >> HTH, >> >> Jim > > > > whops! > > I wasn't familiar with the qc() plots, so I assumed they were straight > plots. Sorry! > > Your idea to just get into the qc() code and add a call to legend as > required seems good and simple enough. > > Is there a function in R that allows you to plot polygons, circles, > etc... *anywhere*? Something similar to 'mtext', only not just for text? > I often multiplot figures, using 'par(mfrow=c(x,y))' among other > suitable parameters to fit several plots consecutively into a larger > figure. Then I use 'mtext' to place text information anywhere in the > final multiplot figure. It works well enough. If there is an equivalent > funtion that you can sue to draw lines, rectangles etc with in teh same > fashion, that would work too. The only functions I know for plotting shapes require (x,y) coordinates, so won't work like mtext(). However, one might be able to come up with a reasonable looking legend just using mtext(). Best, Jim > > Jose -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.