Hi Thomas and Kasper, Many thanks for the tip - I managed to carry out the adjustments I needed in inkscape. I'd still reccomend adding a group label feature to heatplot for general convenience, but modifying in svg format does seem to be a very handy way of finalising things. Forgive my ignorance but what does "out of the box" mean (below)? Best wishes, Amy ________________________________________ From: Kasper Daniel Hansen [khansen@stat.berkeley.edu] Sent: 25 July 2008 20:31 To: Thomas Girke Cc: Mikhail, Amy; 'aedin at jimmy.harvard.edu'; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Adding a text label to the classvec colour bar in heatplot You will be glad to know that as of 2.7 R supports a SVG device out of the box (if compiled with Cairo support). Kasper On Jul 25, 2008, at 8:38 AM, Thomas Girke wrote: > What I find often very helpful for the final refinements of a > heatmaps or > any other graphics generated in R is the possibility to save the plots > in SVG format (Scalable Vector Graphics). This format allows you to > edit all features in an R plot with graphics editors that have SVG > support. > A very nice and free one is InkScape: http://www.inkscape.org/. Adobe > Illustrator should work too. After the import of the SVG file into > InkScape you ungroup the graphics object to make all the changes final > refinements you want. The SVG format is supported by many web > browsers and > it is becoming more and more the default graphics format for community > web projects like Wikipedia. > > Here is a short example: > > library("RSvgDevice") # install package from CRAN > devSVG("test.svg") > plot(1:10, 1:10) > dev.off() > > Thomas > > > On Fri, Jul 25, 2008 at 01:06:28PM +0100, Mikhail, Amy wrote: >> Hi Aedin, >> >> What I'd like to do is add group text labels over the colourbar on >> the top (the rows in my heatplot are genes, the columns are >> samples). If you look at figures 2 or 3 in the paper below which >> is co-authored by Robert Gentleman you can see an example of what I >> mean - the "Relapse" "CCR" labels on the 3rd figure are the type of >> thing I'm after. This paper was written a while ago (2003) so not >> sure if the figures were made with heatplot or something else, but >> I'd be interested to know how it was done? >> >> http://bloodjournal.hematologylibrary.org/cgi/content/abstract/103/ 7/2771 >> >> The dendrogram group labels are not quite what I'm after but it >> would be interesting to see anyway. I think it would be useful if >> heatplot had a straight-forward option to add group labels in this >> way. >> >> Best wishes, >> Amy >> >> -----Original Message----- >> From: Aedin Culhane [mailto:aedin at jimmy.harvard.edu] >> Sent: 25 July 2008 00:02 >> To: bioconductor at stat.math.ethz.ch; Mikhail, Amy >> Subject: Re: Adding a text label to the classvec colour bar in >> heatplot >> >> Dear Amy >> Do you want to add a group text label on each sample, or just over >> the colorbar on the side ? The label on each sample is easy to >> do. Do you want code for this? >> >> However currently I haven't implemented a group text label on >> colorbars in heatplot. I don't think its available in heatmap or >> heatmap.2. >> >> Another function, we have called pretty.dend draws multiple >> colorbars beneath a clustering dendrogram and these colorbars have >> group labels. >> In the development version I used mtext to add the group labels to >> the side of the color bar and this is prettier than the function >> in the current release. >> >> Unfortunately I haven't implemented group labels adjacent to the >> colorbar in heatplot as I would have to write code that doesn't >> call heatmap/heatmap.2. >> >> Let me know if you find an alternative work around, or if you need >> me to modify heatplot. >> >> I can send you the development version of pretty.dend so you can >> see what the output looks like. The output from a modified version >> of heatplot would look very similar (but has the option of >> including a heatmap). >> >> Regards >> Aedin >> >> (and.. BioC developers... I know I should modify pretty.dend so it >> doesn't have a . in the function name... sorry, my mistake, its on >> my to-do list ;-) >> >> >> >> Dear BioCs, >> >> I'm trying to create a heat plot with a matrix containing real time >> PCR data for just 5 genes. There are 105 samples, belonging to 7 >> groups (groups are in numerical order). The matrix looks like this >> (Age is my grouping variable): >> >> Gene1 Gene2 Gene3 Gene4 >> Gene5 Age >> A1R_D03 -13.71434 -14.19288 -15.79439 -14.93712 -14.87174 3 >> A4R_D03 -13.29068 -13.39888 -16.49077 -14.87276 -15.21852 3 >> A7R_D03 -13.19423 -13.09508 -15.80787 -14.59671 -14.47190 3 >> A10R_D03 -13.33472 -13.34051 -15.60396 -14.69521 -14.28135 3 >> A13R_D03 -11.89260 -11.73026 -16.05069 -14.59895 -16.40680 3 >> A61K_D03 -14.64341 -14.55358 -16.37900 -15.44644 -15.80778 3 >> >> ...etc >> >> As there are so many samples, it doesn't make sense to have the >> individual sample names on the graph, so I would like to have the >> samples in their group order with just the seven group labels. >> With heatplot I can get the colourbar for my seven groups using the >> classvec argument, but can't find any way to label the colourbars >> with text... >> >> Also, I'm a little confused about the re-ordering that heatplot >> does - how can I be sure that the samples belonging to a particular >> group are underneath the appropriate colourbar (and given my >> situation I would also want the groups to appear in numerical order)? >> >> I have tried using heatmap.2 as well, but it seems only heatplot >> has the colour bar by group option - heatmap.2 only allows you to >> add a colourbar representing each column separately? >> >> Here is my code: >> >> #(Ngenet is a transposition of my matrix and the Age variable is in >> a separate dataframe so that it doesn't appear directly on the plot). >> >> >>>> heatplot(Ngenet, dend="none", cols.default=FALSE, margin=c(7, 7), >>>> labCol=FALSE, lowcol="red", highcol="green", scale="none", >>>> classvec=Mop$Age) >>> >> >> If anyone could suggest how I might add the group labels, I'd be >> very grateful - appologies if this is something very simple, I have >> actually seen papers with plots showing exactly what I want to do >> but just can't figure out how to do it. >> >> With best wishes, >> Amy >> >> >> >> >> -- >> Aed?n Culhane, >> Research Associate >> Computational Biology and Functional Genomics Laboratory Harvard >> School of Public Health, Dana-Farber Cancer Institute >> >> 44 Binney Street, SM822C >> Department of Biostatistics and Computational Biology, Dana-Farber >> Cancer Institute Boston, MA 02115 USA >> >> Phone: +1 (617) 632 2468 >> Fax: +1 (617) 582 7760 >> Email: aedin at jimmy.harvard.edu >> Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html >> >> >> >> >> The University of Aberdeen is a charity registered in Scotland, No >> SC013683. >> >> _______________________________________________ >> 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 >> > > -- > Thomas Girke > Assistant Professor of Bioinformatics > Director, IIGB Bioinformatic Facility > Center for Plant Cell Biology (CEPCEB) > Institute for Integrative Genome Biology (IIGB) > Department of Botany and Plant Sciences > 1008 Noel T. Keen Hall > University of California > Riverside, CA 92521 > > E-mail: thomas.girke at ucr.edu > Website: http://faculty.ucr.edu/~tgirke > Ph: 951-827-2469 > Fax: 951-827-4437 > > _______________________________________________ > 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 The University of Aberdeen is a charity registered in Scotland, No SC013683.