Dear all, I am trying to create pairs plots with two different panel functions creating MvA and XY scatterplots, respectively. In this context I ran into two problems: 1)I did not manage to assign separate xlim, ylim values to both functions. This is what I tried: panel.mva = function (x, y, ...) { m <- x - y a <- (x + y)/2 ma.plot(a, m, show.statistics = FALSE, span = 2/3, plot.method="add", ylim=c(-4,4)) } panel.lines <- function(x, y, ...) { points(x, y)} pairs(matr[gvIndex, c(1,28)], upper.panel= panel.mva, lower.panel=panel.lines, gap=0, ylim=c(4,14)) Each panel function for itself works just fine outside pairs(), using pairs() I always end up with the same ylim in both upper and lower panel. I tried to look at the code for pairs() and ma.plot() but could not figure out the reason for this. 2)The ma.plot help page indicates that the plot.method argument has to be set to "add" if the MvA plot is to be added to an existing plot like in my case; and indeed, setting it to "smoothScatter", leads to an error message : Error in pairs.default(matr[gvIndex, c(1, 28)], panel = panel.mva) : the 'panel' function made a new plot The MA plot is not positioned properly and 'jumps' to the next matrix position. Is there a possibility to use smoothscatter in conjunction with pairs()? I tried to assign add=T to ma.plot() in my panel.mva function which did not work. Any hints or recommendations would be highly appreciated. Kind regards, Stefan -- Dr. Stefan Thomsen Research Associate Department of Zoology University of Cambridge Downing Street Cambridge CB2 3EJ Tel.: +44 1223 336623 Fax: +44 1223 336679 stt26 at cam.ac.uk

Dear Stefan, > 2)The ma.plot help page indicates that the plot.method argument has to be > set to "add" if the MvA plot is to be added to an existing plot like in my > case; and indeed, setting it to "smoothScatter", leads to an error message > : > > Error in pairs.default(matr[gvIndex, c(1, 28)], panel = panel.mva) : > the 'panel' function made a new plot > > The MA plot is not positioned properly and 'jumps' to the next matrix > position. > > Is there a possibility to use smoothscatter in conjunction with pairs()? I > tried to assign add=T to ma.plot() in my panel.mva function which did not > work. > Have a look at the man page / examples of "smoothScatter" :) -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber