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
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