Hi Al, Nice suggestion, I am still looking for a nice way to present these density plots with the names. So I will think about it with your suggestion. Cheers, Audrey Al Ivens wrote: > Hi Audrey, > > Thanks for the prompt reply. I take your point about split.plots, > although sometimes it IS useful to see everything together! Could the > html report perhaps have a separate graphic with the legend, which might > thus get around the "space on the plot" issue? > > Cheers and thanks, > > a > > >> -----Original Message----- >> From: audrey [mailto:audrey at ebi.ac.uk] >> Sent: 19 December 2007 09:03 >> To: Al Ivens >> Cc: 'bioc' >> Subject: Re: [BioC] arrayQualityMetrics >> >> >> Hi Al, >> >> Thank you for the useful feedback. In the development version of >> arrayQualityMetrics, I have added a legend with the name of the >> experiments on the density and ecdf plots. I will think about >> adding the >> same on the RNAdeg plot in the next version. >> However when there are too many experiments there is not >> enough place on >> the plot to write all the experiment names so I advice you in >> that case >> to use the argument "split.plots" of arrayQualityMetrics and >> to set it >> at 20 maximum. >> >> Thank you, >> Audrey >> >> >> Al Ivens wrote: >> >>> Hi, >>> >>> I have been using arrayQualityMetrics, and find it very useful. >>> However, to make it even more useful, would it be possible to have >>> legends for some of the plots, e.g. density/ecdf, RNAdeg >>> >> incorporated >> >>> in the output? >>> >>> Cheers and thanks, >>> >>> a >>> >>> >>> >>> >>>> sessionInfo() >>>> >>>> >>> R version 2.6.0 (2007-10-03) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >>> Kingdom.1252;LC_MONETARY=English_United >>> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >>> >>> attached base packages: >>> [1] grid splines tools stats graphics >>> >> grDevices utils >> >>> datasets methods base >>> >>> other attached packages: >>> [1] arrayQualityMetrics_1.2.0 latticeExtra_0.3-1 CCl4_1.0.6 >>> simpleaffy_2.14.05 >>> [5] affyPLM_1.14.0 gcrma_2.10.0 >>> matchprobes_1.10.0 RColorBrewer_1.0-2 >>> [9] vsn_3.2.1 limma_2.12.0 affy_1.16.0 >>> preprocessCore_1.0.0 >>> [13] affyio_1.6.1 genefilter_1.16.0 >>> >> survival_2.34 >> >>> geneplotter_1.16.0 >>> [17] lattice_0.17-2 annotate_1.16.1 >>> >> xtable_1.5-2 >> >>> AnnotationDbi_1.0.6 >>> [21] RSQLite_0.6-4 DBI_0.2-4 >>> >> Biobase_1.16.1 >> >>> loaded via a namespace (and not attached): >>> [1] KernSmooth_2.22-21 >>> >>> >>> >>> >>> >>> >>> > > > > >