Perhaps our Genome Graphs tool will do what you want.

http://genome.ucsc.edu/cgi-bin/hgGenome
http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html

-Galt

----- Original Message -----
From: "Louis Letourneau" <[email protected]>
To: [email protected]
Sent: Tuesday, September 29, 2009 11:56:46 AM GMT -08:00 US/Canada Pacific
Subject: [Genome] 2D dot plotting

4 years ago a post was put to plot 2d datas:
https://lists.soe.ucsc.edu/pipermail/genome/2005-September/008529.html

The answer given was to use wiggle, but the format plots bars, is there 
a way now to plot true 2D data like log r ratios or b allele frequencies 
in the browser?

These values range from 0 to 1 for many snps (say for a typical genome 
wide chip nowadays, it could go up to 1,000,000 snps).

Thanks
Louis
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