Hi, plotting the centroids of three parameters with pamr.plotcen() results in tiny "genenames" that can hardly be read and a really weird space consumption in the plot. It looks about that: +------------------------------+ | | | | | | | J N | | | | | | | | | | xxx +----- ---+ | | | | | | xxx +--- --+ | | | | | | xxx +-- -+ | +------------------------------+ There would be enough space for the lower part of the plot (the one containing the centroids and genenames) to be stretched vertically much more. Then the genenames font could be even bigger and more readable. I had a look at the function header of pamr.plotcen() but unfortunately there is no corresponding argument. Is there anyway to get the function plot that thing in a more reasonable fashion? regards Benjamin

Hi Benjamin, Benjamin Otto wrote: > Hi, > > plotting the centroids of three parameters with pamr.plotcen() results in > tiny "genenames" that can hardly be read and a really weird space > consumption in the plot. It looks about that: > > +------------------------------+ > | | > | | > | | > | J N | > | | > | | > | | > | | > | xxx +----- ---+ | > | | | | > | xxx +--- --+ | > | | | | > | xxx +-- -+ | > +------------------------------+ > > There would be enough space for the lower part of the plot (the one > containing the centroids and genenames) to be stretched vertically much > more. Then the genenames font could be even bigger and more readable. I had > a look at the function header of pamr.plotcen() but unfortunately there is > no corresponding argument. Is there anyway to get the function plot that > thing in a more reasonable fashion? The example for pamr.plotcen() doesn't look quite like that, so maybe it has something to do with the number of genes that are being plotted in your case. Anyway, there isn't a variable for the text size, so you will need to modify the code yourself if you want this added functionality (or plead your case with the maintainer, Rob Tibshirani). All you would need to do is add a cex argument (say cex = 0.4), and then modify the last line of the function to read text(rep(0, nd), seq(nd), label = g, cex = cex, adj = 0, col = 1) You can call this function something different like my.pamr.plotcen, save it as my.pamr.plotcen.R, and source() it into your R session. Then call my.pamr.plotcen(<whatever arguments="">, cex = 0.7). HTH, Jim > > regards > > Benjamin > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC 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.