[adegenet-forum] Query about Adegene : How to get snp position plateau curve

[Hiren Ghosh]

Hi I was trying to label off from the plot. Can anyone suggest how to
preceded. I tried like


> plot(clust$g, main="Clusters obtained by gengraph", labels=FALSE)
Error in i.parse.plot.params(graph, list(...)) :
  Unknown plot parameters: labels

[image: Inline images 2]



 Sent with Mailtrack

On 10 January 2017 at 14:56, Thibaut Jombart <thibautjombart at gmail.com>
wrote:
>
> Hi,
>
> what you describe sounds like a complete linkage clustering. What you
wanna do is:
>
> 1) get hamming distances using dist.dna (you got that already)
> 2) use hclust specifying the right method for complete linkage clustering
> 3) use cutree on the resulting dendrogram for a given threshold
>
> Cheers
> Thibaut
>
>
> --
> Dr Thibaut Jombart
> Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
> Head of RECON: repidemicsconsortium.org
> sites.google.com/site/thibautjombart/
> github.com/thibautjombart
> Twitter: @TeebzR
> +44(0)20 7594 3658
>
> On 10 January 2017 at 13:39, Hiren Ghosh <hiren.ghosh at gmail.com> wrote:
>>
>> My data set like this : I have a core genome alignment of 240 e coli
genome, which are varying number of snps from ~0-44200. Now i would like to
clustered  all them according to number of snps. Suppose all the genome
share bellow 100 snps will be one cluster so on all bellow 500 will be one
cluster so on.....
>> Can anyone suggest some idea. how to proceed.
>> Thanks
>>
>>
>>
>>
>>  Sent with Mailtrack
>>
>> On 10 January 2017 at 13:43, Roman Luštrik <roman.lustrik at biolitika.si>
wrote:
>>>
>>> Forwarding this to the list.
>>>
>>> It's not clear to me what you would like to measure. Would like to see,
given a constant cutoff, when clusters don't change much as you add SNPs?
>>>
>>> Cheers,
>>> Roman
>>>
>>>
>>>
>>> ----
>>> In god we trust, all others bring data.
>>>
>>> ________________________________
>>> From: "Hiren Ghosh" <hiren.ghosh at gmail.com>
>>> To: "Roman Luštrik" <roman.lustrik at biolitika.si>
>>> Sent: Tuesday, January 10, 2017 1:33:52 PM
>>> Subject: Re: [adegenet-forum] Query about Adegene : How to get snp
position plateau curve
>>>
>>> Hello,
>>> I am very new to such analysis. Mainly my aim is to cluster based on
the number of mutations separating sequences, classifying them in the same
cluster if their distance is less than a given threshold.
>>> Thanks For reply.
>>> Kind
>>> Hiren
>>>
>>>
>>>
>>>  Sent with Mailtrack
>>>
>>> On 10 January 2017 at 13:25, Roman Luštrik <roman.lustrik at biolitika.si>
wrote:
>>>>
>>>> What statistic are you trying to square off against number of SNPs?
>>>>
>>>> Cheers,
>>>> Roman
>>>>
>>>> ----
>>>> In god we trust, all others bring data.
>>>>
>>>> ________________________________
>>>> From: "Hiren Ghosh" <hiren.ghosh at gmail.com>
>>>> To: adegenet-forum at lists.r-forge.r-project.org
>>>> Sent: Tuesday, January 10, 2017 12:04:25 PM
>>>> Subject: [adegenet-forum] Query about Adegene : How to get snp
position        plateau curve
>>>>
>>>> Hello Developer, Currently i am using your adegent package,  in this
way :
>>>> #data input from multi-genome-alignment file
>>>> dna <- fasta2DNAbin("./core_gene_alignment.fasta")
>>>> D <- dist.dna(dna, model="N")
>>>> clust <- gengraph(D)
>>>>
>>>>
>>>> I would like to have a look how many snps position is there until my
data will be a plateau curve.  . Could you please help me out.
>>>>
>>>>
>>>> Thanks Advance.
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Hiren Ghosh, Doctoral Research Scholar
>>>> Biomedizinisches Forschungszentrum Seltersberg
>>>> Institut für Medizinische Mikrobiologie
>>>> Justus-Liebig-Universität
>>>> Schubertstr. 81
>>>> 35392 Gießen , Germany
>>>>
>>>> Mobile No: 017672157634
>>>>
>>>> Email:hiren.ghosh at med.uni-giessen.de
>>>>
>>>>
>>>>
>>>>
>>>>  Sent with Mailtrack
>>>>
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>>>>
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
>>>
>>>
>>>
>>>
>>> --
>>>
>>> Hiren Ghosh, Doctoral Research Scholar
>>> Biomedizinisches Forschungszentrum Seltersberg
>>> Institut für Medizinische Mikrobiologie
>>> Justus-Liebig-Universität
>>> Schubertstr. 81
>>> 35392 Gießen , Germany
>>>
>>> Mobile No: 017672157634
>>>
>>> Email:hiren.ghosh at med.uni-giessen.de
>>>
>>>
>>
>>
>>
>> --
>>
>> Hiren Ghosh, Doctoral Research Scholar
>> Biomedizinisches Forschungszentrum Seltersberg
>> Institut für Medizinische Mikrobiologie
>> Justus-Liebig-Universität
>> Schubertstr. 81
>> 35392 Gießen , Germany
>>
>> Mobile No: 017672157634
>>
>> Email:hiren.ghosh at med.uni-giessen.de
>>
>>
>> _______________________________________________
>> adegenet-forum mailing list
>> adegenet-forum at lists.r-forge.r-project.org
>>
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
>
>



--

Hiren Ghosh, Doctoral Research Scholar
Biomedizinisches Forschungszentrum Seltersberg
Institut für Medizinische Mikrobiologie
Justus-Liebig-Universität
Schubertstr. 81
35392 Gießen , Germany

Mobile No: 017672157634

Email:hiren.ghosh at med.uni-giessen.de
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