Search
Question: how to reduce the file size of scatter plot matrix
0
gravatar for Caimiao Wei
13.3 years ago by
Caimiao Wei100
Caimiao Wei100 wrote:
Dear all, I am trying to get the scatter plot matrix (function "pairs") and MVA plot (function "mva.pairs") of multiple affy chips. When I use postscript() or pdf() to save the graphs generated from 12 affy mouse chips using the "pairs" function, the size of the file is about 500 MB. I would appreciate any suggestions that can effectively reduces the size of these plots. Caimiao [[alternative HTML version deleted]]
ADD COMMENTlink modified 13.3 years ago by F Duan100 • written 13.3 years ago by Caimiao Wei100
0
gravatar for A.J. Rossini
13.3 years ago by
A.J. Rossini810
A.J. Rossini810 wrote:
"Caimiao Wei" <caimiaow@u.washington.edu> writes: > I am trying to get the scatter plot matrix (function "pairs") and MVA > plot (function "mva.pairs") of multiple affy chips. When I use > postscript() or pdf() to save the graphs generated from 12 affy mouse > chips using the "pairs" function, the size of the file is about 500 > MB. I would appreciate any suggestions that can effectively reduces > the size of these plots. Instead of scatterplots, you might try contour plots. best, -tony -- Anthony Rossini Research Associate Professor rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
ADD COMMENTlink written 13.3 years ago by A.J. Rossini810
0
gravatar for James Wettenhall
13.3 years ago by
James Wettenhall1000 wrote:
Hi, On Mon, 12 Jul 2004, Caimiao Wei wrote: > I am trying to get the scatter plot matrix (function "pairs") > and MVA plot (function "mva.pairs") of multiple affy chips. > When I use postscript() or pdf() to save the graphs generated > from 12 affy mouse chips using the "pairs" function, the size > of the file is about 500 MB. I would appreciate any > suggestions that can effectively reduces the size of these plots. Have a look at the hexbin package (available from Bioconductor) by Dan Carr, Nicholas Lewin-Koh and Martin Maechler. It has a nice vignette, available in you R library directory : hexbin/doc/hexagon_binning.pdf OR http://www.bioconductor.org/repository/devel/vignette/hexagon_binning. pdf Regards, James
ADD COMMENTlink written 13.3 years ago by James Wettenhall1000
Hi Caimiao yet two more options: - use "png" or "jpeg" as an output device. For these the output file size is limited by the number of pixels in the image. - use Jelle Goeman's and Paul Eilers' fast scatterplot smoother http://www.math.leidenuniv.nl/~jgoeman Best wishes Wolfgang James Wettenhall wrote: > On Mon, 12 Jul 2004, Caimiao Wei wrote: > >>I am trying to get the scatter plot matrix (function "pairs") >>and MVA plot (function "mva.pairs") of multiple affy chips. >>When I use postscript() or pdf() to save the graphs generated >>from 12 affy mouse chips using the "pairs" function, the size >>of the file is about 500 MB. I would appreciate any >>suggestions that can effectively reduces the size of these plots. ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber
ADD REPLYlink written 13.3 years ago by Wolfgang Huber13k
0
gravatar for Michael Seewald
13.3 years ago by
Michael Seewald130 wrote:
On Mon, 12 Jul 2004, Caimiao Wei wrote: > I am trying to get the scatter plot matrix (function "pairs") and MVA plot > (function "mva.pairs") of multiple affy chips. When I use postscript() or > pdf() to save the graphs generated from 12 affy mouse chips using the > "pairs" function, the size of the file is about 500 MB. I would appreciate > any suggestions that can effectively reduces the size of these plots. Dear Caimiao, I think the png() command is what you should use. Using postscript() or pdf() will essentially duplicate your data and project it into postscript expressions. If you are only interested in the picture, png() is the way of choice. jpeg() is IMHO not a good alternative, as it will smear out hard contrasts, which are abundant in scientific plots. Best regards, Michael
ADD COMMENTlink written 13.3 years ago by Michael Seewald130
Hi Michael > I think the png() command is what you should use. Using postscript() or pdf() > will essentially duplicate your data and project it into postscript > expressions. If you are only interested in the picture, png() is the way of > choice. jpeg() is IMHO not a good alternative, as it will smear out hard > contrasts, which are abundant in scientific plots. ... while we're talking about image quality: I often use a sequence of commands like dev.copy(pdf, file="img.pdf", height=..., width=...) dev.off() system("convert -density 360 img.pdf -compress RLE img.tif") file.remove("img.pdf") which assumes that the program "convert" from the imageMagick package is in your path and is of course a little clumsy compared to talking to a real device but works well e.g. for inclusion of images in Powerpoint. Best wishes Wolfgang -- ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber
ADD REPLYlink written 13.3 years ago by Wolfgang Huber13k
0
gravatar for F Duan
13.3 years ago by
F Duan100
F Duan100 wrote:
I am using R/Bioconductor under windows. When I want to copy some plot into word or PowerPoint, I often select the option "copy as matfile" instead of "copy as bmp". I don't know if that could serves your needs. Good luck, Duan -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Caimiao Wei Sent: Monday, July 12, 2004 17:53 To: bioconductor@stat.math.ethz.ch Subject: [BioC] how to reduce the file size of scatter plot matrix Dear all, I am trying to get the scatter plot matrix (function "pairs") and MVA plot (function "mva.pairs") of multiple affy chips. When I use postscript() or pdf() to save the graphs generated from 12 affy mouse chips using the "pairs" function, the size of the file is about 500 MB. I would appreciate any suggestions that can effectively reduces the size of these plots. Caimiao [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 13.3 years ago by F Duan100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 172 users visited in the last hour