[genoPlotR-help] GenoPlotR: dna_segs in different directions

[David Williams]

Thanks Lionel, that's perfect.

On 02/28/2012 02:33 AM, Lionel Guy wrote:
> Hi David,
>
> Thanks for your interest in genoPlotR. For the interest of all, I cc
> this email to the mailing list.
>
> On 28 Feb 2012, at 2:09 , David Williams wrote:
>
>> I'm enjoying using you R library genoPlotR. Is it possible to plot
>> different dna_segs in different directions in the same plot? I'm
>> comparing regions on Arachaeal genomes but the ORFs are on
>> different strands. Reversing the starts and ends seems to have no
>> effect i.e., ascending order is automatically plotted.
>
> You should try to use the argument xlims in plot_gene_map. For
> example, say you want to plot segments a, b, c in genome x and d, e
> in genome y. You will use xlims:
>
> xlims<- list(c(10,31,42,56,67,89), c(54,65,78,99))
> plot_gene_maps(dna_segs=list(x,y), comparisons=list(x_vs_y),
> xlims=xlims)
>
> where coordinates of segment a is 10 to 31, of b is 42 to 56, etc. To
> show segments b and e in the other direction, simply invert their
> coordinates:
>
> xlims_inv<- list(c(10,31,56,42,67,89), c(54,65,99,78))
> plot_gene_maps(dna_segs=list(x,y), comparisons=(x_vs_y),
> xlims=xlims_inv)
>
> That should just work fine. Let me know if it doesn't.
>
> Cheers,
>
> Lionel



-- 
David Williams

Post Doctoral Research Fellow
Molecular and Cell Biology
University of Connecticut, USA
http://gogarten.uconn.edu/