[Gmod-help] Re: [Gmod-gbrowse] xyplot - multiple lines

[Haiming Wang]

Hi Dave,

Thanks so much for the detailed summary and suggestion. They are very 
helpful! The hybrid_plot looks really cool and feature-split is a nice 
workaround as well.  I will give it a try and get back to you if  I have 
more questions.

Cheers,
-Haiming


Dave Clements, GMOD Help Desk wrote:
> Hi Haiming,
>
> This request comes up periodically.  From a thread with Neil Saunders in April:
> ------
> I don't think the xyplot glyph was intended to be used to render more
> than one y value per x value.  However, as you found, that doesn't
> mean you can't do it.
>
> Some things to try:
> * Try setting graph_type to line, or linepoints.  It won't look the
> same, but it might fix the overlapping.
> * Peter Ruzanov has created a glyph for displaying 2 sets of data
> points in the same track.  See
> http://modencode.oicr.on.ca/cgi-bin/gbrowse/fly/?start=132050;stop=132940;ref=2L;width=800;version=100;cache=on;drag_and_drop=on;show_tooltips=on;grid=on;id=444a3fbb24fdcc0784c36e2454a472d4;label=Genes-Lai_RNASEQ_DUAL_D
> for an example.
> ** This is called a hybrid_plot and it is based on wiggle_xyplot.
> ** See http://search.cpan.org/~lds/Bio-Graphics/lib/Bio/Graphics/Glyph/hybrid_plot.pm
>
> Peter might be able to shed more light on this glyph.
> -----
>
> Neil eventually did this:
> -----
> In the end, I opted to split my features (microarray probesets)
> equally for each sample type and plot bars.  For example if I have
> expression values of 3 types (normal, adenoma, cancer) across a 1200bp
> probe, I'd split into 3 x 400bp with a different coloured bar at
> 1-400, 401-800 and 801-1200.
> -----
>
> Hope this helps,
>
> Dave C.
>
> On Tue, Aug 18, 2009 at 11:01 AM, Haiming Wang<hwang at uga.edu> wrote:
>   
>> The xyplot is designed to work on a single feature group. I'd like to
>> know if there is a glyph can draw multiple lines - similar to trace
>> glyph instead of taking .scf as input. Thanks,
>>
>> -Haiming
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>     
>
>
>
>