[R] scatterplot of 100000 points and pdf file format

[Witold Eryk Wolski]

Hi,
Yes, indeed the hexbin package generates very cool pix. They look great. 
I was using it already.
But this time I am interested in visualizing exactly the _scatter_ of 
some extreme points.

Eryk

Liaw, Andy wrote:

>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
>>
>>______________________________________________
>>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
>>
>>
>>    
>>
>
>
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-- 
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin
tel: 0049-30-83875219                 __("<    _
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      wolski at molgen.mpg.de