I wish to save a scatter plot comprising approx. 2 million points
in order to include it in a LaTeX document.
Using 'pdf(...)' produces a file of size about 20 MB, which is
useless.
Using 'cairo_pdf(...)' produces a smaller file, around 3 MB. This
is still too large. Not only that the document will be too large,
but also PDF viewers choke on this. Moreover, Cairo has problems
with text: by default text looks ugly, like scaled bitmaps. After
hours of trying different settings, I discovered that choosing a
different font family can help, e.g.: 'par(family="Mono")'.
This
gives good-looking text. Yet, the problem with the file size
remains.
There exists the hint to produdc EPS instead and then convert to
PDF using 'epstopdf'. The resulting PDF files are slightly
smaller, but still too large, and PDF viewers still don't like
it.
So I gave PNG a try. PNG files are much smaller and PDF viewers
have no trouble with them. However, fonts look ugly. The same
trick that worked for Cairo PDF has no effect for PNG. When I
view the PNGs with a dedicated viewer like 'qiv', even the fonts
look good. But not when included in LaTeX; I simply use
'\includegraphics{...}' and run the document through 'pdflatex'.
I tried both, creating PNG with 'png(...)' and converting from
PDF to PNG using 'convert' from ImageMagick.
So my questions are:
- Is there a way to produce sufficiently lean PDFs directly in R,
even when the plot comprises several million points?
- How to produce a PNG that still looks nice when included in a
LaTeX PDF document?
Any hints will be greatly appreciated.
Thank you
Lasse
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Dear Lasse, This won't answer your specific questions and I apologize for that. AFAIK, pdf() produces uncompressed PDFs only. But you could use tools like pdftk to compress your PDFs. About the PNGs, you can always set the 'res' argument to improve resolution, but it won't beat the PDFs. I'm not sure the reader (of your LaTeX document) would be interested in seeing each of the 2M points of your scatter plot and, even if he was, I doubt he could. So, instead of plot(x, y), have you considered using: smoothScatter(x, y) ? Cheers, b On Oct 22, 2009, at 5:07 PM, Lasse Kliemann wrote:> I wish to save a scatter plot comprising approx. 2 million points > in order to include it in a LaTeX document. > > Using 'pdf(...)' produces a file of size about 20 MB, which is > useless. > > Using 'cairo_pdf(...)' produces a smaller file, around 3 MB. This > is still too large. Not only that the document will be too large, > but also PDF viewers choke on this. Moreover, Cairo has problems > with text: by default text looks ugly, like scaled bitmaps. After > hours of trying different settings, I discovered that choosing a > different font family can help, e.g.: 'par(family="Mono")'. This > gives good-looking text. Yet, the problem with the file size > remains. > > There exists the hint to produdc EPS instead and then convert to > PDF using 'epstopdf'. The resulting PDF files are slightly > smaller, but still too large, and PDF viewers still don't like > it. > > So I gave PNG a try. PNG files are much smaller and PDF viewers > have no trouble with them. However, fonts look ugly. The same > trick that worked for Cairo PDF has no effect for PNG. When I > view the PNGs with a dedicated viewer like 'qiv', even the fonts > look good. But not when included in LaTeX; I simply use > '\includegraphics{...}' and run the document through 'pdflatex'. > > I tried both, creating PNG with 'png(...)' and converting from > PDF to PNG using 'convert' from ImageMagick. > > So my questions are: > > - Is there a way to produce sufficiently lean PDFs directly in R, > even when the plot comprises several million points? > > - How to produce a PNG that still looks nice when included in a > LaTeX PDF document? > > Any hints will be greatly appreciated. > > Thank you > Lasse > <ATT00001><ATT00002.txt>
The problem with the pdf files is that they are storing the information for every one of your points, even the ones that are overplotted by other points. The png file is smaller because it only stores information on which color each pixel should be, not how many points contributed to a particular pixel being a given color. But then png files convert the text to pixel information as well which don't look good if there is post scaling. If you want to go the pdf route, then you need to find some way to reduce redundant information while still getting the main points of the plot. With so many point, I would suggest looking at the hexbin package (bioconductor I think) as one approach, it will not be an identical scatterplot, but will convey the information (possibly better) with much smaller graphics file sizes. There are other tools like sunflower plots or others, but hexbin has worked well for me. If you want to go the png route, the problem usually comes from scaling the plot after producing it. So, the solution is to create the plot at the exact size and at the exact resolution that you want to use it at in your document so that no scaling needs to be done. Use the png function, but don't accept the defaults, choose the size and resolution. If you later decide on a different size of graph, recreate the file, don't let LaTeX rescale the first one. Hope this helps, -- 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 Lasse Kliemann > Sent: Thursday, October 22, 2009 1:07 PM > To: r-help at r-project.org > Subject: [R] PDF too large, PNG bad quality > > I wish to save a scatter plot comprising approx. 2 million points > in order to include it in a LaTeX document. > > Using 'pdf(...)' produces a file of size about 20 MB, which is > useless. > > Using 'cairo_pdf(...)' produces a smaller file, around 3 MB. This > is still too large. Not only that the document will be too large, > but also PDF viewers choke on this. Moreover, Cairo has problems > with text: by default text looks ugly, like scaled bitmaps. After > hours of trying different settings, I discovered that choosing a > different font family can help, e.g.: 'par(family="Mono")'. This > gives good-looking text. Yet, the problem with the file size > remains. > > There exists the hint to produdc EPS instead and then convert to > PDF using 'epstopdf'. The resulting PDF files are slightly > smaller, but still too large, and PDF viewers still don't like > it. > > So I gave PNG a try. PNG files are much smaller and PDF viewers > have no trouble with them. However, fonts look ugly. The same > trick that worked for Cairo PDF has no effect for PNG. When I > view the PNGs with a dedicated viewer like 'qiv', even the fonts > look good. But not when included in LaTeX; I simply use > '\includegraphics{...}' and run the document through 'pdflatex'. > > I tried both, creating PNG with 'png(...)' and converting from > PDF to PNG using 'convert' from ImageMagick. > > So my questions are: > > - Is there a way to produce sufficiently lean PDFs directly in R, > even when the plot comprises several million points? > > - How to produce a PNG that still looks nice when included in a > LaTeX PDF document? > > Any hints will be greatly appreciated. > > Thank you > Lasse
On 10/23/2009 06:07 AM, Lasse Kliemann wrote:> I wish to save a scatter plot comprising approx. 2 million points > in order to include it in a LaTeX document. > > Using 'pdf(...)' produces a file of size about 20 MB, which is > useless. > > Using 'cairo_pdf(...)' produces a smaller file, around 3 MB. This > is still too large. Not only that the document will be too large, > but also PDF viewers choke on this. Moreover, Cairo has problems > with text: by default text looks ugly, like scaled bitmaps. After > hours of trying different settings, I discovered that choosing a > different font family can help, e.g.: 'par(family="Mono")'. This > gives good-looking text. Yet, the problem with the file size > remains. > > There exists the hint to produdc EPS instead and then convert to > PDF using 'epstopdf'. The resulting PDF files are slightly > smaller, but still too large, and PDF viewers still don't like > it. > > So I gave PNG a try. PNG files are much smaller and PDF viewers > have no trouble with them. However, fonts look ugly. The same > trick that worked for Cairo PDF has no effect for PNG. When I > view the PNGs with a dedicated viewer like 'qiv', even the fonts > look good. But not when included in LaTeX; I simply use > '\includegraphics{...}' and run the document through 'pdflatex'. > > I tried both, creating PNG with 'png(...)' and converting from > PDF to PNG using 'convert' from ImageMagick. > > So my questions are: > > - Is there a way to produce sufficiently lean PDFs directly in R, > even when the plot comprises several million points? > > - How to produce a PNG that still looks nice when included in a > LaTeX PDF document? > > Any hints will be greatly appreciated. >Hi Lasse, I may be right off the track, but I can't make much sense of 2 million points in a scatterplot. If you are interested in the density of points within the plot, you could compute this using something like the bkde2 function in the KernSmooth package and then plot that using something like "image". Jim