Jocelyn Paine
2010-Aug-31 04:21 UTC
[R] Making plots in big scatterplot matrix large enough to see
I've got a data frame with 23 columns, and wanted to plot a scatterplot
matrix of it. I called
pairs( df )
where 'df' is my data frame. This did generate the matrix, but the
plotting window did not expand to make the individual plots large enough
to see. Each one was only about 10 pixels high and wide.
I tried sending the plot to a file, with a high and wide image,
by doing
png( "plot.png", width = 4000, height = 4000 )
but I got these errors:
Error in png( "plot.png", width = 4000, height = 4000 ) :
unable to start device
In addition: Warning messages:
1: In png( "plot.png", width = 4000, height = 4000 ) :
Unable to allocate bitmap
2: In png( "plot.png", width = 4000, height = 4000 ) :
opening device failed
The messages aren't helpful, because they don't tell you _why_ R
can't
start the device, allocate it, or open it. The documentation for png says:
Windows imposes limits on the size of bitmaps: these are not documented
in the SDK and may depend on the version of Windows. It seems that width
and height are each limited to 2^15-1.
However, 2^15-1 is 32767, so that isn't the problem here. I tried various
values for height and width. 2400 was OK, but 2500 wasn't. So it seems R
can't produce plots that are more than about 2400 pixels square. This is
with R 2.10.1.
Why is png failing on big images? Also, what's the recommended way to make
a file containing a scatterplot matrix when you have lots of variables?
'pairs' is a very useful function, but obviously one does need to be
careful when doing this, and I don't know what experts would recommend. Do
you loop round the variables plotting each pair to a different file? I was
hoping that I could put them all into one very big image and view parts of
it at a time.
Thanks,
Jocelyn Paine
http://www.j-paine.org
http://www.spreadsheet-parts.org
+44 (0)7768 534 091
William Revelle
2010-Aug-31 15:05 UTC
[R] Making plots in big scatterplot matrix large enough to see
Jocelyn, In a partial answer to your question, try setting gap=0 in the calls to pairs. This will make the plots closer together. (You might also find pairs.panels in the psych package useful, -- it implements one of the help examples for pairs to report the histogram on the diagonal and reports the correlations in the upper off diagonal). On a Mac, I just tried setting quartz(width=30, height=30) #make a big graphics window #then library(psych) my.data <- sim.item(24) #create 500 cases of 24 variables pairs.panels(my.data, gap=0) #the gap =0 makes the plots right next to each other #And then save the graphics window as a pdf. I can open this in a pdf and scroll around pretty easily. Bill At 5:21 AM +0100 8/31/10, Jocelyn Paine wrote:>I've got a data frame with 23 columns, and wanted to plot a >scatterplot matrix of it. I called > pairs( df ) >where 'df' is my data frame. This did generate the matrix, but the >plotting window did not expand to make the individual plots large >enough to see. Each one was only about 10 pixels high and wide. > >I tried sending the plot to a file, with a high and wide image, by doing > png( "plot.png", width = 4000, height = 4000 ) >but I got these errors: > Error in png( "plot.png", width = 4000, height = 4000 ) : > unable to start device > In addition: Warning messages: > 1: In png( "plot.png", width = 4000, height = 4000 ) : > Unable to allocate bitmap > 2: In png( "plot.png", width = 4000, height = 4000 ) : > opening device failed > >The messages aren't helpful, because they don't tell you _why_ R >can't start the device, allocate it, or open it. The documentation >for png says: > Windows imposes limits on the size of bitmaps: these are not documented > in the SDK and may depend on the version of Windows. It seems that width > and height are each limited to 2^15-1. >However, 2^15-1 is 32767, so that isn't the problem here. I tried >various values for height and width. 2400 was OK, but 2500 wasn't. >So it seems R can't produce plots that are more than about 2400 >pixels square. This is with R 2.10.1. > >Why is png failing on big images? Also, what's the recommended way >to make a file containing a scatterplot matrix when you have lots of >variables? 'pairs' is a very useful function, but obviously one does >need to be careful when doing this, and I don't know what experts >would recommend. Do you loop round the variables plotting each pair >to a different file? I was hoping that I could put them all into one >very big image and view parts of it at a time. > >Thanks, > >Jocelyn Paine >http://www.j-paine.org >http://www.spreadsheet-parts.org >+44 (0)7768 534 091 > >______________________________________________ >R-help at r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code.-- William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Use R for psychology http://personality-project.org/r It is 6 minutes to midnight http://www.thebulletin.org
Greg Snow
2010-Aug-31 19:49 UTC
[R] Making plots in big scatterplot matrix large enough to see
Look at the pairs2 function in the TeachingDemos package, this lets you produce smaller portions of the total scatterplot matrix at a time (with bigger plots), you could print the smaller portions then assemble the full matrix on a large wall, or just use it to look at potentially interesting parts. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.snow at imail.org 801.408.8111> -----Original Message----- > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r- > project.org] On Behalf Of Jocelyn Paine > Sent: Monday, August 30, 2010 10:21 PM > To: r-help at r-project.org > Subject: [R] Making plots in big scatterplot matrix large enough to see > > I've got a data frame with 23 columns, and wanted to plot a scatterplot > matrix of it. I called > pairs( df ) > where 'df' is my data frame. This did generate the matrix, but the > plotting window did not expand to make the individual plots large > enough > to see. Each one was only about 10 pixels high and wide. > > I tried sending the plot to a file, with a high and wide image, > by doing > png( "plot.png", width = 4000, height = 4000 ) > but I got these errors: > Error in png( "plot.png", width = 4000, height = 4000 ) : > unable to start device > In addition: Warning messages: > 1: In png( "plot.png", width = 4000, height = 4000 ) : > Unable to allocate bitmap > 2: In png( "plot.png", width = 4000, height = 4000 ) : > opening device failed > > The messages aren't helpful, because they don't tell you _why_ R can't > start the device, allocate it, or open it. The documentation for png > says: > Windows imposes limits on the size of bitmaps: these are not > documented > in the SDK and may depend on the version of Windows. It seems that > width > and height are each limited to 2^15-1. > However, 2^15-1 is 32767, so that isn't the problem here. I tried > various > values for height and width. 2400 was OK, but 2500 wasn't. So it seems > R > can't produce plots that are more than about 2400 pixels square. This > is > with R 2.10.1. > > Why is png failing on big images? Also, what's the recommended way to > make > a file containing a scatterplot matrix when you have lots of variables? > 'pairs' is a very useful function, but obviously one does need to be > careful when doing this, and I don't know what experts would recommend. > Do > you loop round the variables plotting each pair to a different file? I > was > hoping that I could put them all into one very big image and view parts > of > it at a time. > > Thanks, > > Jocelyn Paine > http://www.j-paine.org > http://www.spreadsheet-parts.org > +44 (0)7768 534 091 > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code.