[genoPlotR-help] genoPlot R

[Lionel Guy]

Hi Shatavia,

Thanks for using genoPlotR. To be able to answer your question, I would need you to send me the whole code that you are using, including the part where you load the genes and the comparison, and the actual files containing the comparison and the genes. 

Best regards, 

Lionel

> On 18 août 2014, at 19:36, "Morrison, Shatavia Sharday (CDC/OID/NCIRD) (CTR)" <xxh5 at cdc.gov> wrote:
> 
> Hello Lionel,
>  
> I’m running into some issues with the genoPlotR package.  Currently I’m trying to generate a plot similar to the one in the Getting Started with genoplotR manual, quick start page 2.  I’m not interested in generating a phylogenetic tree with the graph image, I just want to show the genes and their corresponding blast results synteny.
>  
> As a test I’m using three genes from two different genomes.  The code listed below generates the attached image. I would like to see the comparisons of the blast results, which are missing.  I have removed the self-hits from the blast results as I thought this is why genoPlotR was not creating the comparisons since there were multiple hits in the file, now that I have removed them I’m still having the same issue.
>  
> What am I missing from my plot gene map function? 
>  
> plot_gene_map(dna_segs = genomeList, comparisons= comparisonList,xlims=xlims,main="Test GenoPlotR", gene_type="arrows",dna_seg_scale= FALSE, scale=TRUE)
>  
> Best,
> Shatavia
> <TestGenoR.tiff>
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