[genoPlotR-help] genoplotR assistance required

[Lionel Guy]

Hi Adnan,

To be sure I got your problem... Could you please send me the commands you are running?

> I have  been trying to use genoPlotR  for some visualizations Since i am beginner in R I have some problems with it. The first problem i am facing is to use tree information. In the barto example, is it the same guided tree which is derived through Mauveprogressive alignment or by other means because when i use Mauve guided tree it gives me error " Tree leaves not corresponding to dna_seg labels".


If you are running genoPlotR with output from Mauve, you might have to change the names. Mauve has the bad habit to replace names by sequence numbers, which may cause your problem. 

If your dna_segs are in the list "ds" and your tree in "tree", compare

names(ds)
names(tree$leaves)

They should be identical (but not necessarily in the same order).

> Secondly, is it possible to show region of interest assume of the genome ranging from 2.5mb to 2.55mb with annotation displayed, by not giving gene names manually as you shown in the example "Several sub-segments of four Bartonella genomes" and "Two segments of the Y chromsome in human and chimp".

To restrict the visualization to some region, use the xlims argument of plot_gene_map.
To annotate your plot, provided that you have gene names in your dna_seg, try to use the function auto_annotate.
I'm not sure I see what you want to do here...

HTH,

Lionel


On 14 Sep 2011, at 9:51 , Adnan Niazi wrote:

> Hej Lionel,
> 
> First of all I thank you and congratulations for the development of much need package for genome representation. I really appreciate it. 
> 
> I have  been trying to use genoPlotR  for some visualizations Since i am beginner in R I have some problems with it. The first problem i am facing is to use tree information. In the barto example, is it the same guided tree which is derived through Mauveprogressive alignment or by other means because when i use Mauve guided tree it gives me error " Tree leaves not corresponding to dna_seg labels".
> 
> Secondly, is it possible to show region of interest assume of the genome ranging from 2.5mb to 2.55mb with annotation displayed, by not giving gene names manually as you shown in the example "Several sub-segments of four Bartonella genomes" and "Two segments of the Y chromsome in human and chimp".
> 
> Your help will be highly appreciated. 
> 
> regards



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Lionel Guy
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