scatterplot of 100000 points and pdf file format

Marc/Eryk,

I have no experience with it, but I believe the hexbin package in BioC was
there for this purpose: avoid heavy over-plotting lots of points.  You might
want to look into that, if you have not done so yet.

Best,
Andy

 

From: Marc Schwartz

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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