[BioC] Gviz DataTrack, type="densityplot"

[Brent Pedersen]

On Thu, Nov 15, 2012 at 1:27 AM, Hahne, Florian
<florian.hahne at novartis.com> wrote:
> Hi Brent,
> There is no particular reason why density plots are nor a standard plot
> type in Gviz. I guess my reasoning was that those would not be necessary
> because the only real application that I see here is for data smoothing,
> and one can already archive that with the 'smooth' plot type. I am happy
> to add this to the next release of Gviz. Thanks for the suggestion.
> Florian
> --
>
>
>
>
>
>
> On 11/13/12 5:13 PM, "Brent Pedersen" <bpederse at gmail.com> wrote:
>
>>Hi, I have been using Gviz to plot some of our methylation data. It is
>>very easy to make detailed figures.
>>I had been plotting the methylation of case vs. control using
>>DataTrack with groups and type="boxplot". I also tried an
>>AnnotationTrack with fun=details, where details is essentially
>>identical to that from the documentation to draw a densityplot. But
>>drawing the density plots gets a bit crowded even if I split them into
>>a couple tracks.
>>
>>Would it be feasible to allow type="densityplot" in DataTrack which
>>would then plot the densityplot rotated 90 degrees. it looks like I
>>could add this in Gviz-methods.R in setMethod("drawGD").
>>I'm not familiar with the lattice stuff, is there a reason that this
>>hasn't been implemented?
>>
>>thanks,
>>-Brent
>


Hi, thanks for the reply. Here's an example where I'm using the densityplot
in detail view to get a better idea of the distribution of the data:
http://www.freeimagehosting.net/6k4i1
It does show essentially the same information as in the boxplot, but
between the rug and
the density, it's actually showing more. IIUC smooth, is across probes, rather
than within probes and across samples within a group.

I had tried for a bit yesterday to add densityplot to DataTrack
to show (rotated 90 degrees) without success.
-B