[R] scatterplot of 100000 points and pdf file format

[Witold Eryk Wolski]

Hi,

I tried the ps idea. But I am using pdflatex.
You get a even larger size reduction if you convert the ps into a pdf 
using ps2pdf.
But unfortunately there is a quality loss.

I have found almost a working solution:
a) Save the scatterplot without axes and with par(mar=c(0,0,0,0)) as png .
b) convert it using any program to pnm
c) read the pnm file using pixmap
d) Add axes labels and lines afterwards with par(new=TRUE)

And this looks like I would like that it looks like. But unfortunately 
acroread and gv on window is crashing when I try to print the file.

png(file="pepslop.png",width=500,height=500)
par(mar=c(0,0,0,0))
X2<-rnorm(100000)
Y2<-X2*10+rnorm(100000)
plot(X2,Y2,pch=".",xlab="",ylab="",main="",axes=F)
dev.off()

pdf(file="pepslop.pdf",width=7,height=7)
par(mar=c(3.2,3.2,1,1))
x <- read.pnm("pepslop.pnm" )
plot(x)
par(new=TRUE)
par(mar=c(3.2,3.2,1,1))
plot(X2,Y2,pch=".",xlab="",ylab="",main="",type="n")
mtext(expression(m[nominal]),side=1,line=2)
mtext(expression(mod(m[monoisotopic],1)),side=2,line=2)
legend(1000,4,expression(paste(lambda[DB],"=",0.000495)),col=2,lty=1,lwd=1)
abline(test,col=2,lwd=2)
dev.off()


 

Marc Schwartz wrote:

>On Wed, 2004-11-24 at 16:34 +0100, Witold Eryk Wolski wrote:
>  
>
>>Hi,
>>
>>I want to draw a scatter plot with 1M  and more points and save it as pdf.
>>This makes the pdf file large.
>>So i tried to save the file first as png and than convert it to pdf. 
>>This looks OK if printed but if viewed e.g. with acrobat as document 
>>figure the quality is bad.
>>
>>Anyone knows a way to reduce the size but keep the quality?
>>    
>>
>
>Hi Eryk!
>
>Part of the problem is that in a pdf file, the vector based instructions
>will need to be defined for each of your 10 ^ 6 points in order to draw
>them.
>
>When trying to create a simple example:
>
>pdf()
>plot(rnorm(1000000), rnorm(1000000))
>dev.off()
>
>The pdf file is 55 Mb in size.
>
>One immediate thought was to try a ps file and using the above plot, the
>ps file was "only" 23 Mb in size. So note that ps can be more efficient.
>
>Going to a bitmap might result in a much smaller file, but as you note,
>the quality does degrade as compared to a vector based image.
>
>I tried the above to a png, then converted to a pdf (using 'convert')
>and as expected, the image both viewed and printed was "pixelated",
>since the pdf instructions are presumably drawing pixels and not vector
>based objects.
>
>Depending upon what you plan to do with the image, you may have to
>choose among several options, resulting in tradeoffs between image
>quality and file size.
>
>If you can create the bitmap file explicitly in the size that you
>require for printing or incorporating in a document, that is one way to
>go and will preserve, to an extent, the overall fixed size image
>quality, while keeping file size small.
>
>Another option to consider for the pdf approach, if it does not
>compromise the integrity of your plot, is to remove any duplicate data
>points if any exist. Thus, you will not need what are in effect
>redundant instructions in the pdf file. This may not be possible
>depending upon the nature of your data (ie. doubles) without considering
>some tolerance level for "equivalence".
>
>Perhaps others will have additional ideas.
>
>HTH,
>
>Marc Schwartz
>
>______________________________________________
>R-help at stat.math.ethz.ch mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
>  
>


-- 
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin
tel: 0049-30-83875219                 __("<    _
http://www.molgen.mpg.de/~wolski      \__/    'v'
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mail: witek96 at users.sourceforge.net    ^^     m m
      wolski at molgen.mpg.de