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.
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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}}
>
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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
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