[genoPlotR-help] GenoPlotR: dna_segs in different directions

[Lionel Guy]

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