[genoPlotR-help] genoPlotR question

[Lionel Guy]

Hi Wei,

Thanks for your interest in genoPlotR.
It's perfectly possible to plot a segment in reverse orientation with genoPlotR. However, the DNA sequence itself is not read by genoPlotR and thus won't be reverse complemented.
The argument to use is xlims, putting first the 3'-end of the segment. From the help page:

     'xlims' allow the user to plot subsegments of a 'dna_seg'. 'xlims'
     consists of a list composed of as many numeric vectors as there
     are segments. Each of these numeric vectors give pairs of left and
     right borders, and gives the direction. For example, c(1,2,6,4)
     will plot two subsegments, segment 1 to 2 which is plotted left to
     right and segment 4 to 6, plotted right to left. '-Inf' and 'Inf'
     values are accepted. 'NULL' values will result in plotting the
     whole segment.

From the examples:

     data("three_genes")
     ## xlims
     ## Just returning a segment
     plot_gene_map(dna_segs, comparisons,
                   xlims=list(NULL, NULL, c(Inf,-Inf)),
                   dna_seg_scale=TRUE)

Note the third element of the xlims list: c(Inf,-Inf) which will plot the whole third segment reversed.

HTH,

Lionel


On 27 Aug 2012, at 4:25 , Wei Lu wrote:

> Dear Lionel,
> 
> Thanks for your great work on this R package. We are now using this tool to help our comparative genomic analysis. I've got a quick question to ask you. Can I do a reverse and complement of dan_seg in genoPlotR? For example, I read a genbank file and plot a 5kb segment of the genome and I would like to reverse and complement this region for the comparison. Can we do this in genoPlotR?
> 
> Thanks,
> 
> Dr. Wei LU
> Research Associate
> University of Western Australia | The Marshall Centre for Infectious
> Diseases Research and Training
> Reception Room 1.2, M Block, QEII Medical Centre | Monash Avenue |
> Nedlands 6009 | Western Australia, Australia.
> T: 08-92876933 | F: 08-92876213 | E: wei.lu at uwa.edu.au
> 

--
Lionel Guy 
Molecular Evolution, Uppsala University, Uppsala, Sweden
postal address: Box 596, SE-751 24 Uppsala; visiting address: BMC C6:305d, Husargatan 3, SE-752 37 Uppsala
phone: +46 18 471 6129, mobile +46 73 976 0618
lionel.guy at icm.uu.se