[genoPlotR-help] GenoplotR

[Lionel Guy]

Dear Gustavo,

Thank you for your interest in genoPlotR.
In read_mauve_backbone, there is an option, common_blocks_only, that is TRUE by default, that discards non-common blocks. Setting it to FALSE should fix your problem. Let me know if it doesn't work...

The reason why it is TRUE by default is that mauve backbone files can be huge and I wanted to limit the size of the objects read by genoPlotR.

HTH,

Lionel

On 8 Mar 2012, at 18:59 , Gustavo Cerqueira wrote:

> Dear Lionel,
> 
> Thanks for the time spent designing GenoplotR. It is a very nice and useful tool for comparative genomics.
> 
> We are having an issue when display Mauve alignments. It seems that only blocks of the backbones with similarity across all genomes are being shown (projections and rainbow plot).
> I mean... All records in Mauve backbbone file with 0 in any of the columns are not being shown. Is this the usual behavior? 
> 
> Thank you very much. Best regards,
> 
> Gustavo
> 
> Gustavo C. Cerqueira, PhD
> Bioinformatics Scientist
> Broad Institute
> 320 Charles Street - Office 2184
> Phone: (617) 714-8469
> E-mail: gustavo at broadinstitute.org
> 

--
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
NEW EMAIL: lionel.guy at icm.uu.se