<div dir="ltr">Hi I was trying to label off from the plot. Can anyone suggest how to preceded. I tried like <div><br></div><div><br>> plot(clust$g, main="Clusters obtained by gengraph", labels=FALSE)<br>Error in i.parse.plot.params(graph, list(...)) : <br> Unknown plot parameters: labels<br><br><img src="cid:ii_1598db087fe1d462" alt="Inline images 2" width="562" height="422"><br><br><br><br> Sent with Mailtrack<br><br>On 10 January 2017 at 14:56, Thibaut Jombart <<a href="mailto:thibautjombart@gmail.com">thibautjombart@gmail.com</a>> wrote:<br>><br>> Hi, <br>><br>> what you describe sounds like a complete linkage clustering. What you wanna do is:<br>><br>> 1) get hamming distances using dist.dna (you got that already)<br>> 2) use hclust specifying the right method for complete linkage clustering<br>> 3) use cutree on the resulting dendrogram for a given threshold<br>><br>> Cheers<br>> Thibaut<br>><br>><br>> --<br>> Dr Thibaut Jombart<br>> Lecturer, Department of Infectious Disease Epidemiology, Imperial College London<br>> Head of RECON: <a href="http://repidemicsconsortium.org">repidemicsconsortium.org</a><br>> <a href="http://sites.google.com/site/thibautjombart/">sites.google.com/site/thibautjombart/</a><br>> <a href="http://github.com/thibautjombart">github.com/thibautjombart</a><br>> Twitter: @TeebzR<br>> +44(0)20 7594 3658<br>><br>> On 10 January 2017 at 13:39, Hiren Ghosh <<a href="mailto:hiren.ghosh@gmail.com">hiren.ghosh@gmail.com</a>> wrote:<br>>><br>>> 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.....<br>>> Can anyone suggest some idea. how to proceed.<br>>> Thanks<br>>> <br>>><br>>><br>>><br>>> Sent with Mailtrack<br>>><br>>> On 10 January 2017 at 13:43, Roman Luštrik <<a href="mailto:roman.lustrik@biolitika.si">roman.lustrik@biolitika.si</a>> wrote:<br>>>><br>>>> Forwarding this to the list.<br>>>><br>>>> 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?<br>>>><br>>>> Cheers,<br>>>> Roman<br>>>><br>>>><br>>>><br>>>> ----<br>>>> In god we trust, all others bring data.<br>>>><br>>>> ________________________________<br>>>> From: "Hiren Ghosh" <<a href="mailto:hiren.ghosh@gmail.com">hiren.ghosh@gmail.com</a>><br>>>> To: "Roman Luštrik" <<a href="mailto:roman.lustrik@biolitika.si">roman.lustrik@biolitika.si</a>><br>>>> Sent: Tuesday, January 10, 2017 1:33:52 PM<br>>>> Subject: Re: [adegenet-forum] Query about Adegene : How to get snp position plateau curve<br>>>><br>>>> Hello, <br>>>> 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. <br>>>> Thanks For reply.<br>>>> Kind<br>>>> Hiren<br>>>><br>>>><br>>>><br>>>> Sent with Mailtrack<br>>>><br>>>> On 10 January 2017 at 13:25, Roman Luštrik <<a href="mailto:roman.lustrik@biolitika.si">roman.lustrik@biolitika.si</a>> wrote:<br>>>>><br>>>>> What statistic are you trying to square off against number of SNPs?<br>>>>><br>>>>> Cheers,<br>>>>> Roman<br>>>>><br>>>>> ----<br>>>>> In god we trust, all others bring data.<br>>>>><br>>>>> ________________________________<br>>>>> From: "Hiren Ghosh" <<a href="mailto:hiren.ghosh@gmail.com">hiren.ghosh@gmail.com</a>><br>>>>> To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>>>>> Sent: Tuesday, January 10, 2017 12:04:25 PM<br>>>>> Subject: [adegenet-forum] Query about Adegene : How to get snp position plateau curve<br>>>>><br>>>>> Hello Developer, Currently i am using your adegent package, in this way :<br>>>>> #data input from multi-genome-alignment file<br>>>>> dna <- fasta2DNAbin("./core_gene_alignment.fasta")<br>>>>> D <- dist.dna(dna, model="N")<br>>>>> clust <- gengraph(D)<br>>>>><br>>>>><br>>>>> 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.<br>>>>><br>>>>><br>>>>> Thanks Advance. <br>>>>><br>>>>><br>>>>><br>>>>><br>>>>> --<br>>>>><br>>>>> Hiren Ghosh, Doctoral Research Scholar<br>>>>> Biomedizinisches Forschungszentrum Seltersberg<br>>>>> Institut für Medizinische Mikrobiologie<br>>>>> Justus-Liebig-Universität<br>>>>> Schubertstr. 81<br>>>>> 35392 Gießen , Germany<br>>>>><br>>>>> Mobile No: 017672157634<br>>>>><br>>>>> <a href="mailto:Email%3Ahiren.ghosh@med.uni-giessen.de">Email:hiren.ghosh@med.uni-giessen.de</a><br>>>>><br>>>>><br>>>>><br>>>>><br>>>>> Sent with Mailtrack<br>>>>><br>>>>> _______________________________________________<br>>>>> adegenet-forum mailing list<br>>>>> <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>>>>> <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum</a><br>>>><br>>>><br>>>><br>>>><br>>>> --<br>>>><br>>>> Hiren Ghosh, Doctoral Research Scholar<br>>>> Biomedizinisches Forschungszentrum Seltersberg<br>>>> Institut für Medizinische Mikrobiologie<br>>>> Justus-Liebig-Universität<br>>>> Schubertstr. 81<br>>>> 35392 Gießen , Germany<br>>>><br>>>> Mobile No: 017672157634<br>>>><br>>>> <a href="mailto:Email%3Ahiren.ghosh@med.uni-giessen.de">Email:hiren.ghosh@med.uni-giessen.de</a><br>>>><br>>>><br>>><br>>><br>>><br>>> --<br>>><br>>> Hiren Ghosh, Doctoral Research Scholar<br>>> Biomedizinisches Forschungszentrum Seltersberg<br>>> Institut für Medizinische Mikrobiologie<br>>> Justus-Liebig-Universität<br>>> Schubertstr. 81<br>>> 35392 Gießen , Germany<br>>><br>>> Mobile No: 017672157634<br>>><br>>> <a href="mailto:Email%3Ahiren.ghosh@med.uni-giessen.de">Email:hiren.ghosh@med.uni-giessen.de</a><br>>><br>>><br>>> _______________________________________________<br>>> adegenet-forum mailing list<br>>> <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>>> <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum</a><br>><br>><br><br><br><br>--<br><br>Hiren Ghosh, Doctoral Research Scholar<br>Biomedizinisches Forschungszentrum Seltersberg<br>Institut für Medizinische Mikrobiologie<br>Justus-Liebig-Universität<br>Schubertstr. 81<br>35392 Gießen , Germany<br><br>Mobile No: 017672157634<br><br><a href="mailto:Email%3Ahiren.ghosh@med.uni-giessen.de">Email:hiren.ghosh@med.uni-giessen.de</a><div class="gmail_extra"><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div>
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