[Genome] 2D dot plotting

[Louis Letourneau]

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

[Galt Barber]

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

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[Hiram Clawson]

Good Afternoon Louis:

Can you provide an example URL to a graph that shows such data ?

Is the X-axis the chromosome position, or some other type of coordinate ?

--Hiram

[Hiram Clawson]

Louis:

Please note the graphing controls on wiggle types of tracks.
You can select to plot the data values as points instead
of a bar graph. If your X axis coordinate is a chromosome
position, and your Y axis coordinate is the value at that
position, you will get a 2D data plot of points.

--Hiram

[Louis Letourneau]

I'm sorry I didn't realize this sooner.
I'll try this out right now.

Thanks
Louis

[Louis Letourneau]

It almost works.

My problem is the "Windowing function". I need to plot every snp at any
zoom level because at higher zoom levels that's when you see patterns of
LOH. If there's a mean, max or min applied I lose this pattern.

Any ideas?

Thanks
Louis

Hiram Clawson wrote:

[Hiram Clawson]

That would be a problem. At this time, I can't plot two different
values in the same "location", where "location" in this sense means
pixel column in the picture. We will have to put this type of
drawing option in our features request queue here. Actually,
we have recently been thinking about new drawing modes for
the wiggle types of tracks, so maybe this will work out sometime
in the nearer future.

--Hiram