So have genomeGraphs making plots I need. BUT have come to a catch; I want to add the genomeGraph plots as part of other plots using the typical layout() command. However the genomeGraphs "plot" command gdPlot() writes a new plot when it is called, or overwrites layout . Can't find options to fix. For example in below I would like to make a plot of x vs X^2 above a genome graphs plot but this fails: ########## get goodies for genome graphs library(GenomeGraphs) mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") minStrand <- makeGeneRegion(chromosome = 17,start = 30450000, end = 30550000,strand = "-", biomart = mart) ideogram <- makeIdeogram(chromosome = 17) genomeAxis <- makeGenomeAxis(add53 = TRUE,add35 = TRUE) #################### nf <- layout(matrix(c(1,2), byrow=TRUE)) layout.show(nf) x<-1:100 y<-x^2 plot(x,y) gdPlot(list(ideogram, plusStrand, genomeAxis, minStrand), minBase = 30450000, maxBase = 30550000) > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-pc-linux-gnu locale: LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomeGraphs_1.4.0 biomaRt_2.0.0 loaded via a namespace (and not attached): [1] lattice_0.17-22 RCurl_0.94-1 tools_2.9.0 XML_1.95-3

Hi Paul this is because GenomeGraphs uses "grid" graphics. The grid graphics system is much more flexible and more consistently designed than R's traditional graphics, and the two do not mix. Have a look into the excellent book "R Graphics" by Paul Murrell, published by Chapman & Hall http://www.amazon.co.uk/Graphics-Computer-Science-Data- Analysis/dp/158488486X Best wishes Wolfgang Paul Leo ha scritto: > So have genomeGraphs making plots I need. BUT have come to a catch; I > want to add the genomeGraph plots as part of other plots using the > typical layout() command. However the genomeGraphs "plot" command > gdPlot() writes a new plot when it is called, or overwrites layout . > Can't find options to fix. > > For example in below I would like to make a plot of x vs X^2 above a > genome graphs plot but this fails: > > > ########## get goodies for genome graphs > library(GenomeGraphs) > mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") > minStrand <- makeGeneRegion(chromosome = 17,start = 30450000, end = > 30550000,strand = "-", biomart = mart) > ideogram <- makeIdeogram(chromosome = 17) > genomeAxis <- makeGenomeAxis(add53 = TRUE,add35 = TRUE) > #################### > > nf <- layout(matrix(c(1,2), byrow=TRUE)) > layout.show(nf) > x<-1:100 > y<-x^2 > plot(x,y) > gdPlot(list(ideogram, plusStrand, genomeAxis, minStrand), minBase = > 30450000, maxBase = 30550000) > > >> sessionInfo() > R version 2.9.0 (2009-04-17) > x86_64-pc-linux-gnu > > locale: > LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_ AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets > methods > [8] base > > other attached packages: > [1] GenomeGraphs_1.4.0 biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] lattice_0.17-22 RCurl_0.94-1 tools_2.9.0 XML_1.95-3 > > _______________________________________________ > 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 -- Best wishes Wolfgang ------------------------------------------------ Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber