eps file export

[Brooke Rhead]

Hi Megan,

You are correct: ever since we changed the menus in the Genome Browser,
the PDF/PS link only shows up on the main image page; it is missing from
Genome Graphs. This is a bug. We will work on fixing it, but in the
meantime, you can still get to the page where you can export .eps files
by altering your URL. If you add "hgGenome_doPsOutput=1" right after
the "?" and add an "&" right after it, you should get to the
"PostScript/PDF Output" screen. Your altered URL will look something
like this:

http://genome.ucsc.edu/cgi-bin/hgGenome?hgGenome_doPsOutput=1&hgsid=301123643&clade=mammal&org=Human&db=hg19&hgGenome_threshold_hg19=3.5&hgGenome_graph_hg19_1_1=ct_UserTrack1_8429&hgGenome_graphColor_hg19_1_1=blue&hgGenome_graph_hg19_1_2=&hgGenome_graphColor_hg19_1_2=red

Thank you for reporting the problem! We apologize for the inconvenience.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Subject: eps file export
From: <mri...@sas.upenn.edu>
Date: 10/3/12 9:52 AM
To: <gen...@soe.ucsc.edu>

Hello,
I have just logged on the browser after a 3 month hiatus and I can not
figure out how to export .eps files of my graphs in genome graphs. The
button that used to be in the upper right hand corner is absent. I can
send a screenshot if you'd like. I have searched the mailing list
archives and can't seem to find anyone else with the same problem. Am I
missing something obvious?

Thanks
Megan

[mri...@sas.upenn.edu]

Hi-

I have a question about Genome Graphs.  I am creating a figure of differentiation across the genome.  I have used genome graphs to view the data (all chromosomes on one line) and I am particularly pleased with it because I can set how close points must be to connect with a line.  That means that the graphs do a good job of showing missing data.  I have saved the graph as a .eps file and tried editing it for print in Illustrator. However, the resolution is insufficient for publication even when the graph is configured to be as large as possible (1200X200).  I am now in the process of recreating a similar graph using R, but I can't find a package that allows for the nice feature of only connecting points that are within some X distance of each other.  Do you know what the code for  genome graphs was based in? Was it all custom scripts?

Thanks
Megan

> Date: Wed, 3 Oct 2012 13:33:45 -0700
> From: rh...@soe.ucsc.edu
> To: mri...@sas.upenn.edu
> CC: Gen...@soe.ucsc.edu
> Subject: eps file export

[Luvina Guruvadoo]

Hi Megan,

To answer your question, yes, genome graphs is based on custom C code. In addition, one of our developers has a few comments on how you may have constructed your GG graph:
If you made a (bed) custom track first, and then imported that into GG, then the resolution will be windowed to 10,000 bases. So one could get a bit higher resolution on GG using its native format without going overboard. If the screen has roughly 1000 pixels, and a large chrom has like 100,000,000 or more pixels, then we expect on the order of 100,000 bases per GG pixel. If the windows are 10k, then you should still see an imported file with a eps/pdf resolution of 10,000 points compare to the screen res of 1,000. And if native GG, then you don't even have that limitation and can go up to 100,000 points or more.

If you have further questions please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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