[genoPlotR-help] error in plot_gene_map with a guide tree

[Lionel Guy]

Hi Zbrel,

The genomes are apparently in a different order in your tree and in your backbone. genoPlotR tries to put them in the same order if the number of label is small. Here it’s not the case, so you have to do the job yourself.

I would recommend that you sort your genomes in the same order as in the tree and input them in mauve in that order. That should help.

Regards,

Lionel

> On 26 Apr 2016, at 9:17 , 童文君 <twj1364992924 at gmail.com> wrote:
> 
> Dear Professor Lionel,
> I'm using your R package "genoPlotR" to visualize my data.
> Before using "genoPlotR" to visualize my data(*.backbone and *.guide_tree), I have used MAUVE to compare 22 prokaryotic genomes(the sizes of genomes range from 6.3Mb to 6.9Mb ).
> When I add a guide tree and plot gene map, there is always an error :
> plot_gene_map(dna_segs=bbone$dna_segs,comparisons=bbone$comparisons,tree=tree,main="Genomes comparison of CFN42 and 21 sequenced strains")
> #Permutation number = 2097152 ( no.over = 1e+05 )
> #Error in permute_tree(tree, dna_seg_labels) : 
> # Number of permutations too large, use a tree that has labels in the same order as dna_segs
> 
> 
> How could I solve this situation ? I'd like to ask you for more suggestion on it.
> Thank you and I'm looking forward to your reply soon.
> Best regards,
> 
> Zbrel
> 
> 
> 
> 
> 

--
Lionel Guy
Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
phone: +46 18 471 4366; mobile +46 73 976 0618; postal address: Box 582, SE-751 23 Uppsala; visiting address: BMC D7:304c, Husargatan 3, SE-752 37 Uppsala
lionel.guy at imbim.uu.se