Hi, I am outputting various plots to pdfs, including heatmaps and the like. What I would like is for the plot to fill the whole of the A4 sheet of paper rather than just a square in the centre. This would increase the readability of a large heatmap no end. Has anyone got any ideas how to achieve this? I am currently using pdf("filename", paper="A4"). Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}

You should take a look at the heatmap.2 function in the gplots package. It has more parameters that can be tweaked. Lynn Daniel Brewer wrote: > Hi, > > I am outputting various plots to pdfs, including heatmaps and the like. > What I would like is for the plot to fill the whole of the A4 sheet of > paper rather than just a square in the centre. This would increase the > readability of a large heatmap no end. Has anyone got any ideas how to > achieve this? > > I am currently using pdf("filename", paper="A4"). > > Thanks > > Dan

If you look at the code for heatmap(), there is a call to layout() with argument respect set to TRUE. Try copying the heatmap() code into your own version and set respect to FALSE (or, maybe you'll have to set respect to a matrix and only set one or some of the entries to 0) I don't know if this will do what you want, but I know I had a similar problem once and something like this did what I wanted. -Ben > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor- > bounces at stat.math.ethz.ch] On Behalf Of Daniel Brewer > Sent: Thursday, March 15, 2007 10:17 AM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] "scale to fit" plot for A4 pdf > > Hi, > > I am outputting various plots to pdfs, including heatmaps and the like. > What I would like is for the plot to fill the whole of the A4 sheet of > paper rather than just a square in the centre. This would increase the > readability of a large heatmap no end. Has anyone got any ideas how to > achieve this? > > I am currently using pdf("filename", paper="A4"). > > Thanks > > Dan > -- > ************************************************************** > > Daniel Brewer, Ph.D. > > Institute of Cancer Research > Email: daniel.brewer at icr.ac.uk > > ************************************************************** > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable > Company Limited by Guarantee, Registered in England under Company No. > 534147 with its Registered Office at 123 Old Brompton Road, London SW7 > 3RP. > > This e-mail message is confidential and for use by the addre...{{dropped}} > > _______________________________________________ > 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 information transmitted in this electronic communication is intended only for the person or entity to whom it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this information in error, please contact the Compliance HelpLine at 800-856-1983 and properly dispose of this information.

Hi Daniel, Daniel Brewer wrote: > Hi, > > I am outputting various plots to pdfs, including heatmaps and the like. > What I would like is for the plot to fill the whole of the A4 sheet of > paper rather than just a square in the centre. This would increase the > readability of a large heatmap no end. Has anyone got any ideas how to > achieve this? > > I am currently using pdf("filename", paper="A4"). From the man page for pdf: Arguments: file: a character string giving the name of the file. For use with 'onefile=FALSE' give a C integer format such as '"Rplot%03d.pdf"' (the default in that case). (See 'postscript' for further details.) width, height: the width and height of the graphics region in inches. The default for width and height is 6, so you will need to increase those values to something sensible for A4 paper. Best, Jim > > Thanks > > Dan -- 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.