[BioC] Question on Gviz

Hahne, Florian florian.hahne at novartis.com
Mon Sep 1 09:10:54 CEST 2014

Hi Alejandro,
You need to provide a little more detail in order for me to help. What
exactly is not working as expected? Can you please provide a simple
reproducible example? Please also provide the output of sessionInfo() for
me to see which package and R version we are talking about.
If your data are available in the form of a rectangular matrix you can
simply provide that to the DataTrack() constructor and play with the
Œgroups¹ display parameter to overlay multiple sample groups on the same
panel. OverlayTrack() is really meant for combining data that is not
rectangular in nature, or when combining different plotting options for
different samples.

From:  Alejandro Berrío <alebesc at gmail.com>
Date:  Sunday 17 August 2014 19:31
To:  Florian Hahne <florian.hahne at novartis.com>
Subject:  Re: Question on Gviz

Hello there,
    I have been working with Gviz for a long time and I am very happy with
it. Thanks for all your work. But I am just curious why the OverlayTrack
and  HighlightTrack functions are not working. I tried to update the
library but it doesn't work as well.
 I am trying to plot two sets of data with same Y and X axis but I haven't
figured out how to combine two DataTracks into 1 without using
Overlaytrack function. I will appreciate any help!

On Thu, Mar 27, 2014 at 3:34 AM, Hahne, Florian
<florian.hahne at novartis.com> wrote:

Hi Alejandro,
Without seeing the structure of your data table I can¹t be very concrete,
but in general the Gviz package should give you all the flexibility you
need in order to create a DataTrack object from it. You may want to
carefully (re-)read the section about
 DataTracks in the package vignette, and also the documentation for the
DataTrack() constructor (by typing '? DataTrack¹). Hopefully this will
already get you much closer to a solution. If you still feel that you are
stuck after doing this home work, please
 send me a reduced example of your conservation table (the first couple of
rows suffice) and I can help you with more concrete code suggestions.

Florian Hahne
Expert Data Integration and Bioinformatics
PCS Informatics
Novartis Pharma AG, NIBR Klybeck
Novartis Institutes for Biomed. Research
Klybeckstrasse 141
CH-4057 Basel

From: Alejandro Berrío <alebesc at gmail.com>
Date: Wednesday 26 March 2014 16:51
To: Florian Hahne <florian.hahne at novartis.com>
Subject: Question on Gviz

Hello Florian,
    I am so excited with the Gviz package. I like it a lot and I hope I
can make some nice genomic graphics. I was wondering if you can help me to
solve a little problem I have. Here is the thing, I am interested in
plotting a track from tabular data via
 converting a phascons conservation table that I downloaded using galaxy
as xxx.tabular which then I modified at the position column from mouse
(mm9) to another species data using a MAFFT alignment.

I can plot the mm9 conservation table using UcscTrack but I cant plot the
modified table I have in my folder because this is not in a datatrack

Is it possible to make the conversion?

I would appreciate any help and thanks in advance!


Alejandro Berrío, PhD Candidate
University of Texas at Austin
www.alejoberrio.com <http://www.alejoberrio.com>

Alejandro Berrío, PhD Candidate
University of Texas at Austin
www.alejoberrio.com <http://www.alejoberrio.com>

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