From t.jombart at imperial.ac.uk Mon Feb 2 14:18:23 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Mon, 2 Feb 2015 13:18:23 +0000 Subject: [adegenet-forum] Hackathon coming: post your feature requests Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABECC472@icexch-m1.ic.ac.uk> Dear all, We need your input! Time to contribute to free scientific software development by saying what you need! Some of you may have heard of a Hackathon for Population Genetics coming up, in NESCent (North Carolina) in next March (http://www.nescent.org/cal/calendar_detail_pg.php?id=1130). The event will focus on improving interoperability between different packages, adapting tools to increasingly large genomic dataset, etc. It will also be the occasion to implement new features in a range of packages, including adegenet. So this is an opportunity for you to post new feature requests. It is very simple to do so: 1) go to this address: http://sourceforge.net/p/adegenet/tickets/ 2) click on 'create a new ticket' 3) fill in the fields of your 'ticket': - title: quick summary of what you want - milestone: select 'next release' - status, owner: leave as default - in the larger text box, provide a description of the feature requested 4) click on 'save', and that's it! Of course there is no guarantee on the outcome, but we'll look at each carefully so it is definitely worth a try. Thanks and all the best Thibaut ps: bug reports welcome too, as always ============================== Dr Thibaut Jombart MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - School of Public Health Norfolk Place, London W2 1PG, UK Tel. : 0044 (0)20 7594 3658 http://sites.google.com/site/thibautjombart/ http://sites.google.com/site/therepiproject/ http://adegenet.r-forge.r-project.org/ Twitter: @thibautjombart -------------- next part -------------- An HTML attachment was scrubbed... URL: From benjamin.alric at univ-lyon1.fr Mon Feb 23 12:06:29 2015 From: benjamin.alric at univ-lyon1.fr (Benjamin Alric) Date: Mon, 23 Feb 2015 12:06:29 +0100 Subject: [adegenet-forum] Simulated hybridization from same locus but with different alleles with hybridize function in adegenet Message-ID: <54EB09B5.4030502@univ-lyon1.fr> Dear all, I would like simulated hybridization between two population to assess the power of admixture analysis (STRUCTURE). I built two subsamples consisting of 30 indivudals showing the highest q values for the cluster1 or cluster2 of previously STRUCTURE analysis. From these two subsamples I would like simulated hybridization (using hybridize function of the adegenet R package) to assess the power of admixture analysis. For each population, genotype were determined through 8 microsatellite loci for wichi one allele is code by a character string of 3 numbers. Here you are the command: Dg<-import2genind("B_Dg.gtx",package="adegenet") Dl<-import2genind("B_Dl.gtx",package="adegenet") Dg<- ##################### ### Genind object ### ##################### - genotypes of individuals - S4 class: genind @call: read.genetix(file = file, missing = missing, quiet = quiet) @tab: 30 x 33 matrix of genotypes @ind.names: vector of 30 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 33 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - Dl<-##################### ### Genind object ### ##################### - genotypes of individuals - S4 class: genind @call: read.genetix(file = file, missing = missing, quiet = quiet) @tab: 30 x 33 matrix of genotypes @ind.names: vector of 30 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 33 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - hybrdis<-hybridize(Dg,Dl,n=100,pop="Hybrids") g1<-genind2df(hybrids) g1<- pop 10_14 Dp512 SwiD1 SwiD10 SwiD12 SwiD14 SwiD15 SwiD5 h001 Hybrids 226226 129 131143 194201 112119 181185 093098 161161165 h002 Hybrids 220226 129 126138 200201 112 175 181181 089098 151153165 h003 Hybrids 220226 129 126134143 200 123123 185185 093098 153163165 h004 Hybrids 220226 129 126131 200201 119123 185185 093098 153153165 h005 Hybrids 220226 129 126136136 199 123123 181185 089098 153161165 h006 Hybrids 226226 129129 136136 194 112112 181181 089098 153161165 h007 Hybrids 220226 129133 134143 194 119 175 181185 093 151153163165 .... We would expect to see two allele for each locus but it is not the case for all microsatellite loci. Somebody know why and where does the problem? I checked the example dataset "microbov" for hybridize function, and I see that temp$Salers and temp$Zebu (used to perform simulated hybridization with hybridize function) presented the same count of alleles at each locus. When I check now my two datasets, I see that there are not the same number of allele between the two populations. such a difference in the number of allele between the two population could be the origne of the problem... Dg at all.names $L1 1 2 3 "220" "226" "231" $L2 1 2 3 "125" "129" "133" $L3 1 2 3 4 5 6 "126" "131" "134" "136" "138" "143" Dl at all.names $L1 1 2 3 "223" "226" "229" $L2 1 2 3 4 5 6 "129" "133" "136" "137" "138" "139" $L3 1 2 3 4 5 6 7 "118" "134" "136" "138" "145" "150" "152" Thank in advence for your help. Sincerely yours, Benjamin ALRIC -- __________________________________________ Benjamin Alric, Post-Doc UMR CNRS 5558 - LBBE "Biom?trie et Biologie Evolutive" UCB Lyon1 Equipe Ecologie Quantitative et Evolutive des Communaut?s B?timent Gr?gor Mendel 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex FRANCE __________________________________________ From benjamin.alric at univ-lyon1.fr Sat Feb 21 17:59:56 2015 From: benjamin.alric at univ-lyon1.fr (Benjamin Alric) Date: Sat, 21 Feb 2015 17:59:56 +0100 Subject: [adegenet-forum] Simulated hybridization from same locus but different alleles with hybridize function and Message-ID: <54E8B98C.2070708@univ-lyon1.fr> Dear all, I would like simulated hybridization between two population to assess the power of admixture analysis (STRUCTURE). I built two subsamples consisting of 30 indivudals showing the highest q values for the cluster1 or cluster2 of previously STRUCTURE analysis. From these two subsamples I would like simulated hybridization (using hybridize function of the adegenet R package) to assess the power of admixture analysis. For each population, genotype were determined through 8 microsatellite loci for wichi one allele is code by a character string of 3 numbers. Here you are the command: Dg<-import2genind("B_Dg.gtx",package="adegenet") Dl<-import2genind("B_Dl.gtx",package="adegenet") Dg<- ##################### ### Genind object ### ##################### - genotypes of individuals - S4 class: genind @call: read.genetix(file = file, missing = missing, quiet = quiet) @tab: 30 x 33 matrix of genotypes @ind.names: vector of 30 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 33 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - Dl<-##################### ### Genind object ### ##################### - genotypes of individuals - S4 class: genind @call: read.genetix(file = file, missing = missing, quiet = quiet) @tab: 30 x 33 matrix of genotypes @ind.names: vector of 30 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 33 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - hybrdis<-hybridize(Dg,Dl,n=100,pop="Hybrids") g1<-genind2df(hybrids) g1<- pop 10_14 Dp512 SwiD1 SwiD10 SwiD12 SwiD14 SwiD15 SwiD5 h001 Hybrids 226226 129 131143 194201 112119 181185 093098 161161165 h002 Hybrids 220226 129 126138 200201 112 175 181181 089098 151153165 h003 Hybrids 220226 129 126134143 200 123123 185185 093098 153163165 h004 Hybrids 220226 129 126131 200201 119123 185185 093098 153153165 h005 Hybrids 220226 129 126136136 199 123123 181185 089098 153161165 h006 Hybrids 226226 129129 136136 194 112112 181181 089098 153161165 h007 Hybrids 220226 129133 134143 194 119 175 181185 093 151153163165 .... We would expect to see two allele for each locus but it is not the case for all microsatellite loci. Somebody know why and where does the problem? I checked the example dataset "microbov" for hybridize function, and I see that temp$Salers and temp$Zebu (used to perform simulated hybridization with hybridize function) presented the same count of alleles at each locus. When I check now my two datasets, I see that there are not the same number of allele between the two populations. such a difference in the number of allele between the two population could be the origne of the problem... Dg at all.names $L1 1 2 3 "220" "226" "231" $L2 1 2 3 "125" "129" "133" $L3 1 2 3 4 5 6 "126" "131" "134" "136" "138" "143" Dl at all.names $L1 1 2 3 "223" "226" "229" $L2 1 2 3 4 5 6 "129" "133" "136" "137" "138" "139" $L3 1 2 3 4 5 6 7 "118" "134" "136" "138" "145" "150" "152" Thank in advence for your help. Sincerely yours, Benjamin ALRIC -- __________________________________________ Benjamin Alric, Post-Doc UMR CNRS 5558 - LBBE "Biom?trie et Biologie Evolutive" UCB Lyon1 Equipe Ecologie Quantitative et Evolutive des Communaut?s B?timent Gr?gor Mendel 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex FRANCE __________________________________________ From Irina.Ilyushkina at vuw.ac.nz Mon Feb 23 05:41:06 2015 From: Irina.Ilyushkina at vuw.ac.nz (Irina Ilyushkina) Date: Mon, 23 Feb 2015 04:41:06 +0000 Subject: [adegenet-forum] scatter plot problem Message-ID: Hi, I'm new to R and would be extremely grateful if someone could help me with my problem. I need to indicate (with labels, with color, etc.) the original group assignment of every individual in the DAPC inferred clusters on the scatter plot. table.value(table(pop(x), grp$grp) is showing the type of plot I'm after but it's a bit confusing when you have to consider two plots at the same time so I'm looking for a way to combine both in one plot if it is possible. Many thanks, Irina -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Mon Feb 23 12:52:25 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Mon, 23 Feb 2015 11:52:25 +0000 Subject: [adegenet-forum] Simulated hybridization from same locus but different alleles with hybridize function and In-Reply-To: <54E8B98C.2070708@univ-lyon1.fr> References: <54E8B98C.2070708@univ-lyon1.fr> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEE3455@icexch-m1.ic.ac.uk> Hi there, the number of alleles shouldn't have to be the same, so I'm not sure what is going on but this might be a bug. May you send a minimum reproducible example (data and commands reproducing the error)? Also, what version of adegenet are you using? Cheers Thibaut ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Benjamin Alric [benjamin.alric at univ-lyon1.fr] Sent: 21 February 2015 16:59 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] Simulated hybridization from same locus but different alleles with hybridize function and Dear all, I would like simulated hybridization between two population to assess the power of admixture analysis (STRUCTURE). I built two subsamples consisting of 30 indivudals showing the highest q values for the cluster1 or cluster2 of previously STRUCTURE analysis. From these two subsamples I would like simulated hybridization (using hybridize function of the adegenet R package) to assess the power of admixture analysis. For each population, genotype were determined through 8 microsatellite loci for wichi one allele is code by a character string of 3 numbers. Here you are the command: Dg<-import2genind("B_Dg.gtx",package="adegenet") Dl<-import2genind("B_Dl.gtx",package="adegenet") Dg<- ##################### ### Genind object ### ##################### - genotypes of individuals - S4 class: genind @call: read.genetix(file = file, missing = missing, quiet = quiet) @tab: 30 x 33 matrix of genotypes @ind.names: vector of 30 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 33 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - Dl<-##################### ### Genind object ### ##################### - genotypes of individuals - S4 class: genind @call: read.genetix(file = file, missing = missing, quiet = quiet) @tab: 30 x 33 matrix of genotypes @ind.names: vector of 30 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 33 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - hybrdis<-hybridize(Dg,Dl,n=100,pop="Hybrids") g1<-genind2df(hybrids) g1<- pop 10_14 Dp512 SwiD1 SwiD10 SwiD12 SwiD14 SwiD15 SwiD5 h001 Hybrids 226226 129 131143 194201 112119 181185 093098 161161165 h002 Hybrids 220226 129 126138 200201 112 175 181181 089098 151153165 h003 Hybrids 220226 129 126134143 200 123123 185185 093098 153163165 h004 Hybrids 220226 129 126131 200201 119123 185185 093098 153153165 h005 Hybrids 220226 129 126136136 199 123123 181185 089098 153161165 h006 Hybrids 226226 129129 136136 194 112112 181181 089098 153161165 h007 Hybrids 220226 129133 134143 194 119 175 181185 093 151153163165 .... We would expect to see two allele for each locus but it is not the case for all microsatellite loci. Somebody know why and where does the problem? I checked the example dataset "microbov" for hybridize function, and I see that temp$Salers and temp$Zebu (used to perform simulated hybridization with hybridize function) presented the same count of alleles at each locus. When I check now my two datasets, I see that there are not the same number of allele between the two populations. such a difference in the number of allele between the two population could be the origne of the problem... Dg at all.names $L1 1 2 3 "220" "226" "231" $L2 1 2 3 "125" "129" "133" $L3 1 2 3 4 5 6 "126" "131" "134" "136" "138" "143" Dl at all.names $L1 1 2 3 "223" "226" "229" $L2 1 2 3 4 5 6 "129" "133" "136" "137" "138" "139" $L3 1 2 3 4 5 6 7 "118" "134" "136" "138" "145" "150" "152" Thank in advence for your help. Sincerely yours, Benjamin ALRIC -- __________________________________________ Benjamin Alric, Post-Doc UMR CNRS 5558 - LBBE "Biom?trie et Biologie Evolutive" UCB Lyon1 Equipe Ecologie Quantitative et Evolutive des Communaut?s B?timent Gr?gor Mendel 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex FRANCE __________________________________________ _______________________________________________ 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 From t.jombart at imperial.ac.uk Mon Feb 23 12:55:52 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Mon, 23 Feb 2015 11:55:52 +0000 Subject: [adegenet-forum] adegenet has moved on GITHUB Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEE3466@icexch-m1.ic.ac.uk> Dear all, after a few years being developed on Sourceforge, adegenet is now on GITHUB: http://github.com/thibautjombart/adegenet This should make bug report, feature requests etc. easier; just use the 'issue' feature: https://github.com/thibautjombart/adegenet/issues This should also make contributing to the package easier. I will update the website when I have time to reflect the change, and give guidance to potential developers / contributors. All the best Thibaut ============================== Dr Thibaut Jombart MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - School of Public Health Norfolk Place, London W2 1PG, UK Tel. : 0044 (0)20 7594 3658 http://sites.google.com/site/thibautjombart/ http://sites.google.com/site/therepiproject/ http://adegenet.r-forge.r-project.org/ Twitter: @thibautjombart -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Mon Feb 23 12:58:53 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Mon, 23 Feb 2015 11:58:53 +0000 Subject: [adegenet-forum] scatter plot problem In-Reply-To: References: Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEE3488@icexch-m1.ic.ac.uk> Hi Irina, I am not sure I understand what you are after, so sorry if I miss the point. If you want to represent a different group to the one used in the DAPC analysis on the DAPC scatterplot, use the argument 'grp'; from ?scatter.dapc: grp: a factor defining group membership for the individuals. The scatterplot is optimal only for the default group, i.e. the one used in the DAPC analysis. Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Irina Ilyushkina [Irina.Ilyushkina at vuw.ac.nz] Sent: 23 February 2015 04:41 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] scatter plot problem Hi, I'm new to R and would be extremely grateful if someone could help me with my problem. I need to indicate (with labels, with color, etc.) the original group assignment of every individual in the DAPC inferred clusters on the scatter plot. table.value(table(pop(x), grp$grp) is showing the type of plot I'm after but it's a bit confusing when you have to consider two plots at the same time so I'm looking for a way to combine both in one plot if it is possible. Many thanks, Irina -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Mon Feb 23 14:30:44 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Mon, 23 Feb 2015 13:30:44 +0000 Subject: [adegenet-forum] Simulated hybridization from same locus but different alleles with hybridize function and In-Reply-To: <54EB200C.9070304@univ-lyon1.fr> References: <54E8B98C.2070708@univ-lyon1.fr> <2CB2DA8E426F3541AB1907F98ABA6570ABEE3455@icexch-m1.ic.ac.uk>, <54EB200C.9070304@univ-lyon1.fr> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEE34F1@icexch-m1.ic.ac.uk> Hi there, it was indeed a bug - fixed now. It will be part of the next release, but meanwhile a patch can be found here: https://github.com/thibautjombart/adegenet/blob/master/pkg/R/hybridize.R Alternatively, you can install the devel version on github using: library(devtools) install_github("thibautjombart/adegenet/pkg") BTW, you probably know this already but Sebastien Devillard, in your department, is the expert of hybridization & STRUCTURE. He can usually be bribed by coffee. Cheers Thibaut ________________________________________ From: Benjamin Alric [benjamin.alric at univ-lyon1.fr] Sent: 23 February 2015 12:41 To: Jombart, Thibaut Subject: Re: [adegenet-forum] Simulated hybridization from same locus but different alleles with hybridize function and Dear Thibaut, Thank you for your response. Firstly, in the dataste example for hybridize function, there is the same number of allele among the two population. Moreover, on other of my dataset, where I have not the same number of allele in eahc loci, I can not made the analysis. A error message said that the two genind object had not the same size. > Dg_1<-import2genind("B_Dg_1.gtx",package="adegenet") Converting data from GENETIX to a genind object... ...done. > Dl_1<-import2genind("B_Dl_1.gtx",package="adegenet") Converting data from GENETIX to a genind object... ...done. > Dg_1 ##################### ### Genind object ### ##################### - genotypes of individuals - S4 class: genind @call: read.genetix(file = file, missing = missing, quiet = quiet) @tab: 30 x 33 matrix of genotypes @ind.names: vector of 30 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 33 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - > Dl_1 ##################### ### Genind object ### ##################### - genotypes of individuals - S4 class: genind @call: read.genetix(file = file, missing = missing, quiet = quiet) @tab: 30 x 32 matrix of genotypes @ind.names: vector of 30 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 32 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - > F1<-hybridize(Dg_1,Dl_1,n=100,pop="Hybrids") Erreur dans Ops.data.frame(tab1, tab2) : ?+? only defined for equally-sized data frames Otherwise, you will find in attached file, a reproductible example dataset in .gtx (B_Dg.gtx and B_Dl.gtx) and commands which reproduced the error. I used adegenet version 1.4-2 on RStudio. Using RStudio can be the source of the problem, for example, because adegraphics for the moment is less supported on RStudio than R. Best regards, Benjamin ALRIC Le 23/02/2015 12:52, Jombart, Thibaut a ?crit : > Hi there, > > the number of alleles shouldn't have to be the same, so I'm not sure what is going on but this might be a bug. > > May you send a minimum reproducible example (data and commands reproducing the error)? Also, what version of adegenet are you using? > > Cheers > Thibaut > > > ________________________________________ > From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Benjamin Alric [benjamin.alric at univ-lyon1.fr] > Sent: 21 February 2015 16:59 > To: adegenet-forum at lists.r-forge.r-project.org > Subject: [adegenet-forum] Simulated hybridization from same locus but different alleles with hybridize function and > > Dear all, > > I would like simulated hybridization between two population to assess > the power of admixture analysis (STRUCTURE). > I built two subsamples consisting of 30 indivudals showing the highest q > values for the cluster1 or cluster2 of previously STRUCTURE analysis. > From these two subsamples I would like simulated hybridization (using > hybridize function of the adegenet R package) to assess the power of > admixture analysis. > For each population, genotype were determined through 8 microsatellite > loci for wichi one allele is code by a character string of 3 numbers. > Here you are the command: > > Dg<-import2genind("B_Dg.gtx",package="adegenet") > Dl<-import2genind("B_Dl.gtx",package="adegenet") > Dg<- ##################### > ### Genind object ### > ##################### > - genotypes of individuals - > > S4 class: genind > @call: read.genetix(file = file, missing = missing, quiet = quiet) > > @tab: 30 x 33 matrix of genotypes > > @ind.names: vector of 30 individual names > @loc.names: vector of 8 locus names > @loc.nall: number of alleles per locus > @loc.fac: locus factor for the 33 columns of @tab > @all.names: list of 8 components yielding allele names for each locus > @ploidy: 2 > @type: codom > > Optional contents: > @pop: factor giving the population of each individual > @pop.names: factor giving the population of each individual > > @other: - empty - > > Dl<-##################### > ### Genind object ### > ##################### > - genotypes of individuals - > > S4 class: genind > @call: read.genetix(file = file, missing = missing, quiet = quiet) > > @tab: 30 x 33 matrix of genotypes > > @ind.names: vector of 30 individual names > @loc.names: vector of 8 locus names > @loc.nall: number of alleles per locus > @loc.fac: locus factor for the 33 columns of @tab > @all.names: list of 8 components yielding allele names for each locus > @ploidy: 2 > @type: codom > > Optional contents: > @pop: factor giving the population of each individual > @pop.names: factor giving the population of each individual > > @other: - empty - > > hybrdis<-hybridize(Dg,Dl,n=100,pop="Hybrids") > g1<-genind2df(hybrids) > g1<- > pop 10_14 Dp512 SwiD1 SwiD10 > SwiD12 SwiD14 SwiD15 SwiD5 > h001 Hybrids 226226 129 131143 194201 112119 > 181185 093098 161161165 > h002 Hybrids 220226 129 126138 200201 112 175 > 181181 089098 151153165 > h003 Hybrids 220226 129 126134143 200 123123 185185 > 093098 153163165 > h004 Hybrids 220226 129 126131 200201 119123 > 185185 093098 153153165 > h005 Hybrids 220226 129 126136136 199 123123 181185 > 089098 153161165 > h006 Hybrids 226226 129129 136136 194 112112 181181 > 089098 153161165 > h007 Hybrids 220226 129133 134143 194 119 175 > 181185 093 151153163165 > .... > > We would expect to see two allele for each locus but it is not the case > for all microsatellite loci. > Somebody know why and where does the problem? > > I checked the example dataset "microbov" for hybridize function, and I > see that temp$Salers and temp$Zebu (used to perform simulated > hybridization with hybridize function) presented the same count of > alleles at each locus. > When I check now my two datasets, I see that there are not the same > number of allele between the two populations. such a difference in the > number of allele between the two population could be the origne of the > problem... > > Dg at all.names > $L1 > 1 2 3 > "220" "226" "231" > > $L2 > 1 2 3 > "125" "129" "133" > > $L3 > 1 2 3 4 5 6 > "126" "131" "134" "136" "138" "143" > > Dl at all.names > $L1 > 1 2 3 > "223" "226" "229" > > $L2 > 1 2 3 4 5 6 > "129" "133" "136" "137" "138" "139" > > $L3 > 1 2 3 4 5 6 7 > "118" "134" "136" "138" "145" "150" "152" > > Thank in advence for your help. > > Sincerely yours, > > Benjamin ALRIC > > > > -- > __________________________________________ > Benjamin Alric, Post-Doc > UMR CNRS 5558 - LBBE > "Biom?trie et Biologie Evolutive" > UCB Lyon1 > Equipe Ecologie Quantitative et Evolutive des Communaut?s > B?timent Gr?gor Mendel > 43 bd du 11 novembre 1918 > 69622 Villeurbanne Cedex > FRANCE > __________________________________________ > > _______________________________________________ > 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 -- __________________________________________ Benjamin Alric, Post-Doc UMR CNRS 5558 - LBBE "Biom?trie et Biologie Evolutive" UCB Lyon1 Equipe Ecologie Quantitative et Evolutive des Communaut?s B?timent Gr?gor Mendel 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex FRANCE __________________________________________ From t.jombart at imperial.ac.uk Mon Feb 23 18:29:08 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Mon, 23 Feb 2015 17:29:08 +0000 Subject: [adegenet-forum] Simulated hybridization from same locus but different alleles with hybridize function and In-Reply-To: <54EB4726.4040604@univ-lyon1.fr> References: <54E8B98C.2070708@univ-lyon1.fr> <2CB2DA8E426F3541AB1907F98ABA6570ABEE3455@icexch-m1.ic.ac.uk>, <54EB200C.9070304@univ-lyon1.fr> <2CB2DA8E426F3541AB1907F98ABA6570ABEE34E5@icexch-m1.ic.ac.uk>, <54EB4726.4040604@univ-lyon1.fr> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEE458E@icexch-m1.ic.ac.uk> Hi there, yes, sorry there was a typo - the one you flagged. Fixed now. Cheers Thibaut ________________________________ From: Benjamin Alric [benjamin.alric at univ-lyon1.fr] Sent: 23 February 2015 15:28 To: Jombart, Thibaut Subject: Re: [adegenet-forum] Simulated hybridization from same locus but different alleles with hybridize function and Dear Thibault, Thanks a lot for your response. I load the new version of hybridize function by the patch founde here: https://github.com/thibautjombart/adegenet/blob/master/pkg/R/hybridize.R However, the function does not work and there was the followinf error message: hybrids<-hybridize(Dg,Dl,n=100,pop="hybrids") Erreur dans nLoc(x) : erreur d'?valuation de l'argument 'x' lors de la s?lection d'une m?thode pour la fonction 'nLoc' : Erreur : objet 'x' introuvable In the source code there is: ## used variables n1 <- nInd(x1) n2 <- nInd(x2) k <- nLoc(x) I found no specification of "x" in your command. nLoc corresponds to number of loci, is it right? But, we should specify where go search the number of loci, is it right? Therefore, I replaced x by x1 in k<-nLoc(x1) and I run the analysis. Now, it works with the results below: hybrids<-hybridize(Dg,Dl,n=100,pop="hybrids") g1<-genind2df(hybrids) g1 pop 10_14 Dp512 SwiD10 SwiD1 SwiD12 SwiD14 SwiD15 SwiD5 h001 hybrids 223226 129137 184201 134150 112116 185187 080089 129153 h002 hybrids 223226 129138 184194 138138 114119 185185 076098 129161 h003 hybrids 223226 129133 191201 126150 112114 175183 076093 137163 h004 hybrids 226226 129138 184194 138138 114119 179187 076093 129165 h005 hybrids 223226 129133 184194 118138 116123 181187 076093 129161 h006 hybrids 223226 129138 190201 118134 114123 183185 076093 129161 h007 hybrids 226226 129133 190201 143150 114123 181185 076089 129161 h008 hybrids 223226 129133 190201 118136 114123 181185 076093 129161 h009 hybrids 223226 129138 184201 138143 114123 185185 076093 129163 h010 hybrids 223226 129137 182201 138138 114119 179187 076089 129163 So, I don't know if you have leave deliberately x instead of x1 but could you tell me if put x1 instead fo x in the function is right. Sorry for the goings and comings. Best regards, Benjamin Le 23/02/2015 14:30, Jombart, Thibaut a ?crit : Hi there, it was indeed a bug - fixed now. It will be part of the next release, but meanwhile a patch can be found here: https://github.com/thibautjombart/adegenet/blob/master/pkg/R/hybridize.R Alternatively, you can install the devel version on github using: library(devtools) install_github("thibautjombart/adegenet/pkg") BTW, you probably know this already but Sebastien Devillard, in your department, is the expert of hybridization & STRUCTURE. He can usually be bribed by coffee. Cheers Thibaut ________________________________________ From: Benjamin Alric [benjamin.alric at univ-lyon1.fr] Sent: 23 February 2015 12:41 To: Jombart, Thibaut Subject: Re: [adegenet-forum] Simulated hybridization from same locus but different alleles with hybridize function and Dear Thibaut, Thank you for your response. Firstly, in the dataste example for hybridize function, there is the same number of allele among the two population. Moreover, on other of my dataset, where I have not the same number of allele in eahc loci, I can not made the analysis. A error message said that the two genind object had not the same size. > Dg_1<-import2genind("B_Dg_1.gtx",package="adegenet") Converting data from GENETIX to a genind object... ...done. > Dl_1<-import2genind("B_Dl_1.gtx",package="adegenet") Converting data from GENETIX to a genind object... ...done. > Dg_1 ##################### ### Genind object ### ##################### - genotypes of individuals - S4 class: genind @call: read.genetix(file = file, missing = missing, quiet = quiet) @tab: 30 x 33 matrix of genotypes @ind.names: vector of 30 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 33 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - > Dl_1 ##################### ### Genind object ### ##################### - genotypes of individuals - S4 class: genind @call: read.genetix(file = file, missing = missing, quiet = quiet) @tab: 30 x 32 matrix of genotypes @ind.names: vector of 30 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 32 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - > F1<-hybridize(Dg_1,Dl_1,n=100,pop="Hybrids") Erreur dans Ops.data.frame(tab1, tab2) : ?+? only defined for equally-sized data frames Otherwise, you will find in attached file, a reproductible example dataset in .gtx (B_Dg.gtx and B_Dl.gtx) and commands which reproduced the error. I used adegenet version 1.4-2 on RStudio. Using RStudio can be the source of the problem, for example, because adegraphics for the moment is less supported on RStudio than R. Best regards, Benjamin ALRIC Le 23/02/2015 12:52, Jombart, Thibaut a ?crit : Hi there, the number of alleles shouldn't have to be the same, so I'm not sure what is going on but this might be a bug. May you send a minimum reproducible example (data and commands reproducing the error)? Also, what version of adegenet are you using? Cheers Thibaut ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Benjamin Alric [benjamin.alric at univ-lyon1.fr] Sent: 21 February 2015 16:59 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] Simulated hybridization from same locus but different alleles with hybridize function and Dear all, I would like simulated hybridization between two population to assess the power of admixture analysis (STRUCTURE). I built two subsamples consisting of 30 indivudals showing the highest q values for the cluster1 or cluster2 of previously STRUCTURE analysis. From these two subsamples I would like simulated hybridization (using hybridize function of the adegenet R package) to assess the power of admixture analysis. For each population, genotype were determined through 8 microsatellite loci for wichi one allele is code by a character string of 3 numbers. Here you are the command: Dg<-import2genind("B_Dg.gtx",package="adegenet") Dl<-import2genind("B_Dl.gtx",package="adegenet") Dg<- ##################### ### Genind object ### ##################### - genotypes of individuals - S4 class: genind @call: read.genetix(file = file, missing = missing, quiet = quiet) @tab: 30 x 33 matrix of genotypes @ind.names: vector of 30 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 33 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - Dl<-##################### ### Genind object ### ##################### - genotypes of individuals - S4 class: genind @call: read.genetix(file = file, missing = missing, quiet = quiet) @tab: 30 x 33 matrix of genotypes @ind.names: vector of 30 individual names @loc.names: vector of 8 locus names @loc.nall: number of alleles per locus @loc.fac: locus factor for the 33 columns of @tab @all.names: list of 8 components yielding allele names for each locus @ploidy: 2 @type: codom Optional contents: @pop: factor giving the population of each individual @pop.names: factor giving the population of each individual @other: - empty - hybrdis<-hybridize(Dg,Dl,n=100,pop="Hybrids") g1<-genind2df(hybrids) g1<- pop 10_14 Dp512 SwiD1 SwiD10 SwiD12 SwiD14 SwiD15 SwiD5 h001 Hybrids 226226 129 131143 194201 112119 181185 093098 161161165 h002 Hybrids 220226 129 126138 200201 112 175 181181 089098 151153165 h003 Hybrids 220226 129 126134143 200 123123 185185 093098 153163165 h004 Hybrids 220226 129 126131 200201 119123 185185 093098 153153165 h005 Hybrids 220226 129 126136136 199 123123 181185 089098 153161165 h006 Hybrids 226226 129129 136136 194 112112 181181 089098 153161165 h007 Hybrids 220226 129133 134143 194 119 175 181185 093 151153163165 .... We would expect to see two allele for each locus but it is not the case for all microsatellite loci. Somebody know why and where does the problem? I checked the example dataset "microbov" for hybridize function, and I see that temp$Salers and temp$Zebu (used to perform simulated hybridization with hybridize function) presented the same count of alleles at each locus. When I check now my two datasets, I see that there are not the same number of allele between the two populations. such a difference in the number of allele between the two population could be the origne of the problem... Dg at all.names $L1 1 2 3 "220" "226" "231" $L2 1 2 3 "125" "129" "133" $L3 1 2 3 4 5 6 "126" "131" "134" "136" "138" "143" Dl at all.names $L1 1 2 3 "223" "226" "229" $L2 1 2 3 4 5 6 "129" "133" "136" "137" "138" "139" $L3 1 2 3 4 5 6 7 "118" "134" "136" "138" "145" "150" "152" Thank in advence for your help. Sincerely yours, Benjamin ALRIC -- __________________________________________ Benjamin Alric, Post-Doc UMR CNRS 5558 - LBBE "Biom?trie et Biologie Evolutive" UCB Lyon1 Equipe Ecologie Quantitative et Evolutive des Communaut?s B?timent Gr?gor Mendel 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex FRANCE __________________________________________ _______________________________________________ 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 -- __________________________________________ Benjamin Alric, Post-Doc UMR CNRS 5558 - LBBE "Biom?trie et Biologie Evolutive" UCB Lyon1 Equipe Ecologie Quantitative et Evolutive des Communaut?s B?timent Gr?gor Mendel 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex FRANCE __________________________________________ -- __________________________________________ Benjamin Alric, Post-Doc UMR CNRS 5558 - LBBE "Biom?trie et Biologie Evolutive" UCB Lyon1 Equipe Ecologie Quantitative et Evolutive des Communaut?s B?timent Gr?gor Mendel 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex FRANCE __________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuel.wicker at cirad.fr Tue Feb 24 11:54:28 2015 From: emmanuel.wicker at cirad.fr (Emmanuel WICKER) Date: Tue, 24 Feb 2015 14:54:28 +0400 Subject: [adegenet-forum] Help : DAPC and Supplementary individuals Message-ID: <54EC5864.4080204@cirad.fr> Dear all, I first performed a DAPC on a worlwide dataset genotyped using 8 microsat loci. Then I tried to inject in this analysis supplementary individuals , genotyped with all same 8 loci. The error message says that "the number of variables does not match original data". The loci are the same in both datasets, can anyone help me find what is going wrong ? Cheers Manu -- *Emmanuel WICKER*, PhD Phytopathologiste / Plant Pathologist /CIRAD, UMR Peuplements V??g??taux et Bioagresseurs en Milieu Tropical (PVBMT)/ P??le de Protection des Plantes 7, chemin de l'IRAT F-97410 Saint Pierre La R??union, France wicker at cirad.fr SITE WEB PVBMT *Tel* : +262 (0) 262 49 92 42 *Fax* : +262 (0) 262 49 92 93 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- ### Importation of a worldwide collection mlva8=read.table("wc_mlva8.txt", header=T, sep="\t", row.names=1) m8<-df2genind(mlva8[,1:8],missing=0, ploidy=1, ncode=2, type="codom") m8$other<-mlva8[,9:13] m8$pop<-m8$other$CC.13 m8$pop.names<-levels(m8$other$CC) #1. find.clusters############# grp.8<-find.clusters(m8, max.n.clust=20) ##DAPC with m8 (the find.clusters was already done) dapc3<-dapc(m8, n.pca=11, grp.8$grp) ###Importation of new populations col<-read.table("col_mlva8.txt",header=T, sep="\t", row.names=1) ##We extract only Vallon 2012,Pirogue_2007. col.mv<-col[col$Collection %in% c("Pirogue_2007","VALLON_2012"),] col.mv$Collection<-factor(col.mv$Collection) col.mv$Habitat<-factor(col.mv$Habitat) col.mv$Country<-factor(col.mv$Country) #2.Importation in format genind col8<-df2genind(col.mv[,1:8],pop=as.factor(col.mv[,9]), missing=0, ploidy=1, ncode=2, type="codom") col8$other<-col.mv[,9:13] col8$pop.names<-levels(col.mv$Collection) ## 4. Injecting supplementary individuals dapc.sup<-predict.dapc(dapc3,newdata=col8)## #RESPONSE: Error in predict.dapc(dapc3, newdata = col8) : ## Number of variables in newdata does not match original data. -------------- next part -------------- Souche CMmp0131 GMch0754 CMmp0233 GMch0133 GMch3461 RS3L20 GMmp0266 Ymp0875 CC.13 Year Country POP Region RS.09.28 0 4 6 1 2 23 5 15 I-CC10 2009 Niger NIGER AFRICA RUN0044 5 7 0 8 2 18 6 15 I-S 1966 Australia AUSTRALIA AUSTR-ASIA RUN0054 3 16 6 5 7 15 10 15 I-S 1978 French_Guiana F_GUIANA SoAMER RUN0100 7 5 6 2 2 18 12 15 I-CC06 1974 Kenya KENYA AFRICA RUN0104 7 6 6 1 2 18 12 15 I-CC06 1986 South_Africa SoAFR AFRICA RUN0119 7 9 6 2 2 14 6 15 I-CC02 2005 Cameroon CAM AFRICA RUN0139 7 3 6 2 2 14 6 15 I-CC03 2005 Cameroon CAM AFRICA RUN0155 12 9 6 2 2 16 6 15 I-CC05 2003 Taiwan TAIWAN ASIA RUN0159 12 9 6 1 2 16 6 15 I-CC05 2003 Taiwan TAIWAN ASIA RUN0205 7 3 6 1 2 14 6 15 I-CC03 2005 Cameroon CAM AFRICA RUN0215 9 8 6 2 2 14 5 15 I-CC02 2005 Cameroon CAM AFRICA RUN0337 9 9 6 1 2 12 4 15 I-CC02 NA China CHINA ASIA RUN0993 3 14 6 7 6 14 5 15 I-CC04 1998 South_Africa SoAFR AFRICA RUN1041 3 14 6 7 6 14 9 15 I-CC04 1997 South_Africa SoAFR AFRICA RUN1051 3 14 6 7 6 14 9 15 I-CC04 1997 South_Africa SoAFR AFRICA RUN1528 13 14 6 5 2 19 7 15 I-S 2004 Guatemala GUAT SoAMER RUN1531 7 0 6 2 2 18 11 15 I-CC06 2010 Ivory_Coast Song AFRICA RUN1533 11 5 7 8 2 17 6 15 I-CC07 2010 Ivory_Coast Song AFRICA RUN1535 11 14 6 4 2 19 7 15 I-CC08 2010 Ivory_Coast Song AFRICA RUN1537 7 5 6 2 2 18 12 15 I-CC06 2010 Ivory_Coast Song AFRICA RUN1538 11 14 6 4 2 19 7 15 I-CC08 2010 Ivory_Coast Song AFRICA RUN1539 7 5 6 2 2 18 11 15 I-CC06 2010 Ivory_Coast Song AFRICA RUN1540 11 5 7 8 2 17 3 15 I-CC07 2010 Ivory_Coast Song AFRICA RUN1739 10 5 7 2 2 28 6 15 I-CC11 2010 Ivory_Coast Bonouf AFRICA RUN1747 11 4 6 2 2 23 5 15 I-CC10 2010 Ivory_Coast Sinf AFRICA RUN1767 10 8 6 2 2 5 6 15 I-CC01 2010 Ivory_Coast Song AFRICA RUN1773 9 5 7 1 2 29 6 15 I-CC11 2010 Ivory_Coast Soua AFRICA RUN1821 10 8 6 1 2 5 6 15 I-CC01 2010 Ivory_Coast Man AFRICA RUN1878 9 4 6 2 2 25 5 15 I-CC10 2011 Ivory_Coast Pak AFRICA RUN1891 9 5 7 2 2 26 0 15 I-CC11 2011 Ivory_Coast Sinf AFRICA RUN1901 9 0 7 2 2 27 6 15 I-CC11 2011 Ivory_Coast Sinf AFRICA RUN1908 10 15 6 4 2 19 7 15 I-CC09 2011 Ivory_Coast Yam AFRICA RUN1909 10 15 6 4 2 19 6 15 I-CC09 2011 Ivory_Coast Yam AFRICA RUN1910 10 15 6 4 2 18 7 15 I-CC09 2011 Ivory_Coast Yam AFRICA -------------- next part -------------- RUN_ID CMmp0131 GMch0754 CMmp0233 GMch0133 GMch3461 RS3L20 GMmp0266 Ymp0875 Collection Habitat Location Country Year Haplotype RUN0715 4 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H004 RUN0717 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0718 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0720 4 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H004 RUN0724 3 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H002 RUN0731 4 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H004 RUN0735 3 12 6 4 7 16 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H001 RUN0737 4 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H004 RUN0738 4 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H004 RUN0740 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0749 4 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H004 RUN0751 4 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H004 RUN0752 4 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H004 RUN0753 3 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H003 RUN0757 3 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H003 RUN0758 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0778 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0783 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0792 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0793 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0798 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0800 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0803 4 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H004 RUN0804 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0805 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0807 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0814 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0820 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0822 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0826 4 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H004 RUN0829 4 12 6 4 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H004 RUN0830 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0834 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0835 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0837 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0838 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN0839 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 RUN1065 4 12 6 5 7 15 10 15 Pirogue_2007 Soil Le_Lorrain Martinique 2007 H005 JV1043 6 5 6 0 2 17 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H012 JV1045 7 5 6 0 2 17 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H013 JV1046 6 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H010 JV1047 6 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H010 JV1049 6 5 6 0 2 17 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H012 JV1053 6 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H010 JV1054 7 5 6 0 2 17 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H013 JV1058 6 5 6 0 2 17 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H012 JV1060 7 5 6 0 2 17 9 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H007 JV1061 6 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H010 JV1062 6 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H010 JV1063 6 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H010 JV1065 6 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H010 JV1067 6 5 6 0 2 17 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H012 JV1068 6 5 6 0 2 17 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H012 JV1069 6 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H010 JV1072 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1075 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1078 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1080 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1082 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1083 7 5 6 0 2 18 9 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H009 JV1154 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1155 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1156 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1157 7 5 6 0 2 18 12 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H011 JV1165 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1166 7 5 6 0 2 18 12 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H011 JV1167 7 5 6 0 2 18 12 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H011 JV1168 7 5 6 0 2 18 12 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H011 JV1169 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1171 7 5 6 0 2 18 12 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H011 JV1177 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1179 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1183 7 5 6 0 2 18 12 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H011 JV1185 7 5 6 0 2 18 12 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H011 JV1186 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1188 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1190 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1191 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1192 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1193 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1196 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1199 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1205 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1208 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1210 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1212 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1213 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1216 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1217 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1218 7 5 6 0 2 18 11 15 VALLON_1999 Stem Le_Vallon Reunion_Island 1999 H008 JV1224 7 5 6 0 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H008 JV1228 7 5 6 0 2 18 12 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H011 JV1229 7 5 6 0 2 18 12 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H011 JV1230 7 5 6 0 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H008 JV1232 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1233 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1237 7 5 6 0 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H008 JV1240 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1242 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1244 7 5 6 0 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H008 JV1248 7 5 6 0 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H008 JV1250 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1254 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1257 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1259 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1260 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1261 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1262 6 4 6 7 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H006 JV1263 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1264 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1265 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1266 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1267 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1268 7 5 6 0 2 18 12 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H011 JV1269 7 5 6 0 2 18 12 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H011 JV1271 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1273 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1274 6 5 6 0 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H010 JV1276 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1277 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1279 7 5 6 0 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H008 JV1282 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1284 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1285 6 5 6 0 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H010 JV1288 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1289 7 5 6 0 2 18 12 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H011 JV1292 7 5 6 0 2 18 12 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H011 JV1293 7 5 6 0 2 18 12 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H011 JV1305 7 5 6 0 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H008 JV1306 7 5 6 0 2 18 12 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H011 JV1309 7 5 6 0 2 18 11 15 VALLON_1999 Rhizosphere Le_Vallon Reunion_Island 1999 H008 JV1314 7 5 6 0 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H008 JV1317 7 5 6 0 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H008 JV1318 7 5 6 0 2 18 11 15 VALLON_1999 Soil Le_Vallon Reunion_Island 1999 H008 RUN1548 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1549 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1550 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1553 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1554 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1558 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1559 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1560 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1563 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1564 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1565 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1569 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1570 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1571 6 5 6 0 3 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H016 RUN1573 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1574 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1575 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1578 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1579 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1583 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1586 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1588 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1589 6 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H015 RUN1597 7 5 6 0 2 18 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H011 RUN1598 7 5 6 0 2 18 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H011 RUN1599 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1600 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1602 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1605 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1607 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1608 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1609 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1610 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1612 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1614 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1615 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1619 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1621 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1622 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1624 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1625 6 5 6 0 2 19 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H014 RUN1629 7 5 6 0 2 18 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H011 RUN1630 7 5 6 0 2 18 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H011 RUN1639 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1640 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1641 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1645 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1646 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1647 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1654 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1655 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1656 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1661 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1662 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1664 7 5 6 0 2 18 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H011 RUN1666 7 5 6 0 2 18 12 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H011 RUN1669 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1670 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1674 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1675 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1679 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1680 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1684 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1685 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1689 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1690 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1694 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1695 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1701 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1702 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1704 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1705 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1706 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1709 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1710 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1714 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1716 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1717 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1719 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1720 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1721 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1724 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1725 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1726 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1730 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1731 7 5 6 0 2 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H009 RUN1732 7 5 6 0 3 18 9 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H017 RUN1734 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1735 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 RUN1736 7 5 6 0 2 18 11 15 VALLON_2009 Stem Le_Vallon Reunion_Island 2009 H008 SM28.17 7 5 6 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H056 SM28.18 7 5 6 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H056 SM28.19 7 5 6 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H056 SM28.20 6 5 6 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H026 SM28.21 7 5 6 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H056 SM28.22 7 5 6 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H056 SM28.23 7 5 6 0 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H008 SM28.24 7 5 6 0 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H008 SM28.25 7 5 6 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H056 SM28.26 9 5 6 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H041 SM37.01 6 5 6 1 2 19 12 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H055 SM37.02 6 5 6 1 2 19 12 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H055 SM37.03 6 5 6 1 2 19 12 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H055 SM37.04 6 5 6 1 2 19 12 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H055 SM37.05 6 5 6 1 2 19 2 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H050 SM37.06 6 5 6 0 2 19 12 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H014 SM37.07 6 5 6 1 2 19 2 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H050 SM37.08 6 5 6 1 2 19 2 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H050 SM37.09 6 5 6 1 2 19 2 12 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H049 SM37.10 6 5 6 1 2 19 2 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H050 SM37.11 6 5 6 1 2 19 2 11 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H044 SM37.13 6 5 6 1 2 19 2 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H050 SM37.14 6 5 6 1 2 19 12 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H055 SM37.15 6 5 6 0 2 19 2 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H048 SM37.17 6 5 6 1 2 19 12 12 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H053 SM37.18 6 5 6 1 2 19 12 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H055 SM37.19 6 5 6 1 2 19 12 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H055 SM37.20 6 5 6 1 2 19 2 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H050 SM37.21 6 5 6 1 2 19 12 12 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H053 SM37.22 6 5 6 1 2 19 12 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H055 SM37.23 5 4 9 7 2 19 12 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H019 SM37.25 6 5 6 1 2 19 12 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H055 SM37.26 6 5 6 1 2 19 12 12 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H053 SP17.01 7 5 6 1 2 18 11 11 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H054 SP17.02 7 5 6 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H056 SP17.03 7 5 6 1 2 18 11 11 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H054 SP17.04 7 5 6 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H056 SP17.05 7 5 9 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H040 SP17.07 7 5 6 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H056 SP17.09 7 5 6 1 2 18 11 11 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H054 SP27.01 7 5 6 1 2 18 11 11 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H054 SP27.02 7 5 6 1 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H056 SP27.03 7 5 6 1 2 18 11 11 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H054 SP27.04 7 5 6 1 2 18 11 11 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H054 SP27.05 7 5 6 0 2 18 11 15 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H008 SP27.06 7 5 6 1 2 18 11 11 VALLON_2012 Soil Le_Vallon Reunion_Island 2012 H054 SP27.08 7 5 6 1 2 18 11 11 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TR22.13 7 5 6 1 2 18 11 11 VALLON_2012 Stem Le_Vallon Reunion_Island 2012 H054 TR22.14 7 5 6 1 2 18 11 15 VALLON_2012 Stem Le_Vallon Reunion_Island 2012 H056 TR22.15 7 5 6 1 2 18 11 11 VALLON_2012 Stem Le_Vallon Reunion_Island 2012 H054 TR22.16 7 5 6 0 2 18 11 11 VALLON_2012 Stem Le_Vallon Reunion_Island 2012 H052 TR22.18 7 5 6 1 2 18 11 11 VALLON_2012 Stem Le_Vallon Reunion_Island 2012 H054 TR22.19 7 5 6 1 2 18 11 15 VALLON_2012 Stem Le_Vallon Reunion_Island 2012 H056 TR22.20 7 5 6 1 2 18 11 11 VALLON_2012 Stem Le_Vallon Reunion_Island 2012 H054 RS.09.28 0 4 6 1 2 23 5 15 WORLDWIDE NA Kollo Niger 2009 H057 RUN0044 5 7 0 8 2 18 6 15 WORLDWIDE NA Queensland_(Nambour) Australia 1966 H074 RUN0054 3 16 6 5 7 15 10 15 WORLDWIDE NA Kourou French_Guiana 1978 H072 RUN0100 7 5 6 2 2 18 12 15 WORLDWIDE NA Mombassa Kenya 1974 H089 RUN0104 7 6 6 1 2 18 12 15 WORLDWIDE NA Transvaal South_Africa 1986 H079 RUN0119 7 9 6 2 2 14 6 15 WORLDWIDE NA Obala_(ZAE5) Cameroon 2005 H080 RUN0139 7 3 6 2 2 14 6 15 WORLDWIDE NA Obala_(ZAE5) Cameroon 2005 H078 RUN0155 12 9 6 2 2 16 6 15 WORLDWIDE NA Yunlin_(West) Taiwan 2003 H068 RUN0157 4 0 6 2 2 14 7 15 WORLDWIDE NA Tainan_(South_West) Taiwan 1988 H073 RUN0159 12 9 6 1 2 16 6 15 WORLDWIDE NA Yunlin_(West) Taiwan 2003 H067 RUN0205 7 3 6 1 2 14 6 15 WORLDWIDE NA Yaounde_(ZAE5) Cameroon 2005 H077 RUN0215 9 8 6 2 2 14 5 15 WORLDWIDE NA Bafia_(ZAE5) Cameroon 2005 H085 RUN0337 9 9 6 1 2 12 4 15 WORLDWIDE NA Nanning,_Guangxi_province China NA H086 RUN0993 3 14 6 7 6 14 5 15 WORLDWIDE NA Petoseed/Hygrotech_BW_field_trial_site South_Africa 1998 H071 RUN1041 3 14 6 7 6 14 9 15 WORLDWIDE NA Transvaal_Lowveld South_Africa 1997 H088 RUN1051 3 14 6 7 6 14 9 15 WORLDWIDE NA Transvaal_Lowveld South_Africa 1997 H088 RUN1528 13 14 6 5 2 19 7 15 WORLDWIDE NA Monjas,_Jalapa Guatemala 2004 H069 RUN1531 7 0 6 2 2 18 11 15 WORLDWIDE Stem Songon_P7 Ivory_Coast 2010 H075 RUN1533 11 5 7 8 2 17 6 15 WORLDWIDE Stem Songon_P7 Ivory_Coast 2010 H066 RUN1535 11 14 6 4 2 19 7 15 WORLDWIDE Stem Songon_P8 Ivory_Coast 2010 H087 RUN1537 7 5 6 2 2 18 12 15 WORLDWIDE Stem Songon_P8 Ivory_Coast 2010 H089 RUN1538 11 14 6 4 2 19 7 15 WORLDWIDE Stem Songon_P8 Ivory_Coast 2010 H087 RUN1539 7 5 6 2 2 18 11 15 WORLDWIDE Stem Songon_P8 Ivory_Coast 2010 H018 RUN1540 11 5 7 8 2 17 3 15 WORLDWIDE Stem Songon_P8 Ivory_Coast 2010 H065 RUN1739 10 5 7 2 2 28 6 15 WORLDWIDE Stem Bonoufla Ivory_Coast 2010 H061 RUN1747 11 4 6 2 2 23 5 15 WORLDWIDE Stem Sinfra_P1 Ivory_Coast 2010 H064 RUN1767 10 8 6 2 2 5 6 15 WORLDWIDE Stem Songon Ivory_Coast 2010 H063 RUN1773 9 5 7 1 2 29 6 15 WORLDWIDE Stem Souandala_P1 Ivory_Coast 2010 H083 RUN1821 10 8 6 1 2 5 6 15 WORLDWIDE Stem Man Ivory_Coast 2010 H062 RUN1878 9 4 6 2 2 25 5 15 WORLDWIDE Stem Pakobo_(Tiassal?) Ivory_Coast 2011 H082 RUN1891 9 5 7 2 2 26 0 15 WORLDWIDE Stem Sinfra Ivory_Coast 2011 H084 RUN1901 9 0 7 2 2 27 6 15 WORLDWIDE Stem Sinfra Ivory_Coast 2011 H081 RUN1908 10 15 6 4 2 19 7 15 WORLDWIDE Stem Yamoussoukro_Zatta_ Ivory_Coast 2011 H060 RUN1909 10 15 6 4 2 19 6 15 WORLDWIDE Stem Yamoussoukro_Zatta_ Ivory_Coast 2011 H059 RUN1910 10 15 6 4 2 18 7 15 WORLDWIDE Stem Yamoussoukro_Zatta_ Ivory_Coast 2011 H058 RUN1955 3 14 6 5 7 15 10 15 WORLDWIDE Stem Montsin?ry French_Guiana 2011 H070 RUN1985 7 18 6 2 2 14 5 15 WORLDWIDE Stem Javouhey French_Guiana 2011 H076 From t.jombart at imperial.ac.uk Wed Feb 25 11:53:35 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Wed, 25 Feb 2015 10:53:35 +0000 Subject: [adegenet-forum] scatter plot problem In-Reply-To: References: , <2CB2DA8E426F3541AB1907F98ABA6570ABEE3488@icexch-m1.ic.ac.uk>, Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEE5A17@icexch-m1.ic.ac.uk> Hello, so I had understood the question, and given you the answer - use the 'pop' argument in ?scatter.dapc. Cheers Thibaut ________________________________ From: Irina Ilyushkina [Irina.Ilyushkina at vuw.ac.nz] Sent: 24 February 2015 22:42 To: Jombart, Thibaut Subject: RE: scatter plot problem I'm sorry for double posting but I'm afraid my Outlook might have failed to include the images in the e-mail. Hi, Thank you very much for the reply! I'm sorry I didn't explain everything clearer. Initially I have 2 populations and they form 3 clusters in DAPC, here is the scatterplot I get with command "scatter(dapc_data, posi.da="bottomleft", bg="white", pch=17:22, scree.da=FALSE, col=myCol)" [cid:7fbe74d8-9d03-420b-a8dd-d913fb75500c] the assignment to the clusters didn't match my population structure perfectly so I need to indicate the origin (which one of 2 initial populations) of each individual in the clusters. I made 2 plots manually in Photoshop to represent my idea better: [cid:859dc59a-2be3-4fa9-8b39-08413fa5b536] or an easier to read color representation: [cid:fddf3b1d-c165-41a8-86b0-b374fab1d57f] Many thanks, Irina Irina Ilyushkina PhD Candidate School of Biological Sciences Victoria University of Wellington P O Box 600 Wellington 6140 New Zealand Mobile: 0223898085 Tel: 04 463 5233 Ext 8135 ________________________________ From: Jombart, Thibaut [t.jombart at imperial.ac.uk] Sent: Tuesday, 24 February 2015 12:58 a.m. To: Irina Ilyushkina; adegenet-forum at lists.r-forge.r-project.org Subject: RE: scatter plot problem Hi Irina, I am not sure I understand what you are after, so sorry if I miss the point. If you want to represent a different group to the one used in the DAPC analysis on the DAPC scatterplot, use the argument 'grp'; from ?scatter.dapc: grp: a factor defining group membership for the individuals. The scatterplot is optimal only for the default group, i.e. the one used in the DAPC analysis. Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Irina Ilyushkina [Irina.Ilyushkina at vuw.ac.nz] Sent: 23 February 2015 04:41 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] scatter plot problem Hi, I'm new to R and would be extremely grateful if someone could help me with my problem. I need to indicate (with labels, with color, etc.) the original group assignment of every individual in the DAPC inferred clusters on the scatter plot. table.value(table(pop(x), grp$grp) is showing the type of plot I'm after but it's a bit confusing when you have to consider two plots at the same time so I'm looking for a way to combine both in one plot if it is possible. Many thanks, Irina -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pomap2_opt1_nooutl_scatter20.jpeg Type: image/jpeg Size: 163399 bytes Desc: pomap2_opt1_nooutl_scatter20.jpeg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Rplotcolors.jpg Type: image/jpeg Size: 40201 bytes Desc: Rplotcolors.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Rpotlabels.jpg Type: image/jpeg Size: 44019 bytes Desc: Rpotlabels.jpg URL: From massimiliano.virgilio at africamuseum.be Wed Feb 25 11:54:20 2015 From: massimiliano.virgilio at africamuseum.be (Virgilio Massimiliano) Date: Wed, 25 Feb 2015 10:54:20 +0000 Subject: [adegenet-forum] DAPC "reduced" confidence ellipse Message-ID: good morning, I have a nice scatter graph of my dapc: scatter(dapc348_country, col=myColCountry, clabel=.5, bg="grey", cellipse=2.5, scree.pca=TRUE, ratio.pca=0.15, scree.da=TRUE, ratio.da=0.15, cstar=1, axesell=FALSE, cex=1, grid=FALSE, addaxes=TRUE) what I would like to do is to re-draw one of the confidence ellipses by excluding a few outliers from one of the populations and possibly show all ellipses calculated for each population + the ?reduced? ellipse calculated on the population with excluded outliers I?m not sure this is really possible though? many thanks in advance for your answer all the best Massi -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Wed Feb 25 13:52:56 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Wed, 25 Feb 2015 12:52:56 +0000 Subject: [adegenet-forum] DAPC "reduced" confidence ellipse In-Reply-To: References: Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEE5AC4@icexch-m1.ic.ac.uk> Hi Massi, tough one! For this kind of customisation you'd have to calculate the ellipse manually. To figure out how it's done in ade4, check out the code of s.class, and scatterutil.ellipse. Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Virgilio Massimiliano [massimiliano.virgilio at africamuseum.be] Sent: 25 February 2015 10:54 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] DAPC "reduced" confidence ellipse good morning, I have a nice scatter graph of my dapc: scatter(dapc348_country, col=myColCountry, clabel=.5, bg="grey", cellipse=2.5, scree.pca=TRUE, ratio.pca=0.15, scree.da=TRUE, ratio.da=0.15, cstar=1, axesell=FALSE, cex=1, grid=FALSE, addaxes=TRUE) what I would like to do is to re-draw one of the confidence ellipses by excluding a few outliers from one of the populations and possibly show all ellipses calculated for each population + the ?reduced? ellipse calculated on the population with excluded outliers I?m not sure this is really possible though? many thanks in advance for your answer all the best Massi -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Wed Feb 25 14:02:41 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Wed, 25 Feb 2015 13:02:41 +0000 Subject: [adegenet-forum] Help : DAPC and Supplementary individuals In-Reply-To: <54EC5864.4080204@cirad.fr> References: <54EC5864.4080204@cirad.fr> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEE5AE1@icexch-m1.ic.ac.uk> Hi there, the variables are alleles here, not only markers. To ensure that your datasets have the same alleles, use the function repool to merge the two datasets, run the DAPC on the chosen subset, and then use the rest as supplementary individuals. Makes sense? Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Emmanuel WICKER [emmanuel.wicker at cirad.fr] Sent: 24 February 2015 10:54 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] Help : DAPC and Supplementary individuals Dear all, I first performed a DAPC on a worlwide dataset genotyped using 8 microsat loci. Then I tried to inject in this analysis supplementary individuals , genotyped with all same 8 loci. The error message says that "the number of variables does not match original data". The loci are the same in both datasets, can anyone help me find what is going wrong ? Cheers Manu -- Emmanuel WICKER, PhD Phytopathologiste / Plant Pathologist CIRAD, UMR Peuplements V??g??taux et Bioagresseurs en Milieu Tropical (PVBMT) P??le de Protection des Plantes 7, chemin de l'IRAT F-97410 Saint Pierre La R??union, France wicker at cirad.fr SITE WEB PVBMT Tel : +262 (0) 262 49 92 42 Fax : +262 (0) 262 49 92 93 -------------- next part -------------- An HTML attachment was scrubbed... URL: From maria.david.salas at gmail.com Wed Feb 25 13:43:03 2015 From: maria.david.salas at gmail.com (Maria del Carmen David) Date: Wed, 25 Feb 2015 07:43:03 -0500 Subject: [adegenet-forum] scatter plot problem In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA6570ABEE5A17@icexch-m1.ic.ac.uk> References: <2CB2DA8E426F3541AB1907F98ABA6570ABEE3488@icexch-m1.ic.ac.uk> <2CB2DA8E426F3541AB1907F98ABA6570ABEE5A17@icexch-m1.ic.ac.uk> Message-ID: Hi, Irina. Back in September I had a similar question. Caitlin Collins wrote some codes to label individuals. If might be what you were looking for. Message from Caitlin Collins: If you think the individuals you are plotting are spaced far enough that you will be able to read labels at the individual level, one way to do it is to use s.label. Here is an example of how to use s.label to overlap labels to a scatterplot of DAPC: ############# ## EXAMPLE ## ############# set.seed(14) # generate a simulated dataset with 3 populations simpop <- glSim(100, 500, 5, k=3, sort.pop=TRUE) # isolate the SNPs and the population factor snps <- as.matrix(simpop) phen <- simpop at other$ancestral.pops # run a dapc dapc1 <- dapc(snps, phen, n.pca=20, n.da=4) # create the scatter plot as before scatter(dapc1, cstar=0, cex=5, label=NULL) # change graphical parameter to subsequently overlay the labels without drawing a new plot par(new=TRUE) # make a data frame of the dapc coordinates used in scatter df <- data.frame(x = dapc1$ind.coord[,1], y = dapc1$ind.coord[,2]) # identify/ create a vector of names for the individuals in your plot noms <- paste("ind", c(1:100), sep=".") # use the text function to add labels to the positions given by the coordinates you used in plot s.label(dfxy = df, xax=1, yax=2, label=noms, clabel=0.7, # change the size of the labels boxes=TRUE, # if points are spaced wide enough, can use TRUE to add boxes around the labels grid=FALSE, addaxes=FALSE) # do not draw lines or axes in addition to the labels On Wed, Feb 25, 2015 at 5:53 AM, Jombart, Thibaut wrote: > > Hello, > > so I had understood the question, and given you the answer - use the 'pop' > argument in ?scatter.dapc. > > Cheers > Thibaut > ------------------------------ > *From:* Irina Ilyushkina [Irina.Ilyushkina at vuw.ac.nz] > *Sent:* 24 February 2015 22:42 > *To:* Jombart, Thibaut > *Subject:* RE: scatter plot problem > > I'm sorry for double posting but I'm afraid my Outlook might have > failed to include the images in the e-mail. > > Hi, > > Thank you very much for the reply! I'm sorry I didn't explain everything > clearer. Initially I have 2 populations and they form 3 clusters in DAPC, > here is the scatterplot I get with command "scatter(dapc_data, > posi.da="bottomleft", bg="white", pch=17:22, scree.da=FALSE, col=myCol)" > > the assignment to the clusters didn't match my population structure > perfectly so I need to indicate the origin (which one of 2 initial > populations) of each individual in the clusters. > > I made 2 plots manually in Photoshop to represent my idea better: > > > > > or an easier to read color representation: > > > > > > > Many thanks, > > Irina > > Irina Ilyushkina > > PhD Candidate > School of Biological Sciences > Victoria University of Wellington > P O Box 600 > Wellington 6140 > New Zealand > > Mobile: 0223898085 > Tel: 04 463 5233 Ext 8135 > ------------------------------ > *From:* Jombart, Thibaut [t.jombart at imperial.ac.uk] > *Sent:* Tuesday, 24 February 2015 12:58 a.m. > *To:* Irina Ilyushkina; adegenet-forum at lists.r-forge.r-project.org > *Subject:* RE: scatter plot problem > > > Hi Irina, > > I am not sure I understand what you are after, so sorry if I miss the > point. If you want to represent a different group to the one used in the > DAPC analysis on the DAPC scatterplot, use the argument 'grp'; from > ?scatter.dapc: > > grp: a factor defining group membership for the individuals. The > scatterplot is optimal only for the default group, i.e. the > one used in the DAPC analysis. > > Cheers > Thibaut > > > ------------------------------ > *From:* adegenet-forum-bounces at lists.r-forge.r-project.org [ > adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Irina > Ilyushkina [Irina.Ilyushkina at vuw.ac.nz] > *Sent:* 23 February 2015 04:41 > *To:* adegenet-forum at lists.r-forge.r-project.org > *Subject:* [adegenet-forum] scatter plot problem > > Hi, > > I'm new to R and would be extremely grateful if someone could help me > with my problem. I need to indicate (with labels, with color, etc.) the > original group assignment of every individual in the DAPC inferred clusters > on the scatter plot. table.value(table(pop(x), grp$grp) is showing the type > of plot I'm after but it's a bit confusing when you have to consider two > plots at the same time so I'm looking for a way to combine both in one plot > if it is possible. > > Many thanks, > > Irina > > _______________________________________________ > 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 > -- Maria del Carmen David Salas -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Rplotcolors.jpg Type: image/jpeg Size: 40201 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: pomap2_opt1_nooutl_scatter20.jpeg Type: image/jpeg Size: 163399 bytes Desc: not available URL: From massimiliano.virgilio at africamuseum.be Thu Feb 26 07:44:06 2015 From: massimiliano.virgilio at africamuseum.be (Virgilio Massimiliano) Date: Thu, 26 Feb 2015 06:44:06 +0000 Subject: [adegenet-forum] DAPC "reduced" confidence ellipse In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA6570ABEE5AC4@icexch-m1.ic.ac.uk> References: <2CB2DA8E426F3541AB1907F98ABA6570ABEE5AC4@icexch-m1.ic.ac.uk> Message-ID: <1609F6DE-58AB-4CA3-8B9A-4190A468002B@africamuseum.be> many thanks I?ll give it a try :-) all the best M. __________________________________ Massimiliano Virgilio, PhD Royal Museum for Central Africa Joint Experimental Molecular Unit (JEMU) Leuvensesteenweg 13, B-3080 Tervuren, Belgium, +32 (0) 27695366 massimiliano.virgilio at africamuseum.be http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/ http://jemu.myspecies.info On 25 Feb 2015, at 13:56, Jombart, Thibaut > wrote: Hi Massi, tough one! For this kind of customisation you'd have to calculate the ellipse manually. To figure out how it's done in ade4, check out the code of s.class, and scatterutil.ellipse. Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Virgilio Massimiliano [massimiliano.virgilio at africamuseum.be] Sent: 25 February 2015 10:54 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] DAPC "reduced" confidence ellipse good morning, I have a nice scatter graph of my dapc: scatter(dapc348_country, col=myColCountry, clabel=.5, bg="grey", cellipse=2.5, scree.pca=TRUE, ratio.pca=0.15, scree.da=TRUE, ratio.da=0.15, cstar=1, axesell=FALSE, cex=1, grid=FALSE, addaxes=TRUE) what I would like to do is to re-draw one of the confidence ellipses by excluding a few outliers from one of the populations and possibly show all ellipses calculated for each population + the ?reduced? ellipse calculated on the population with excluded outliers I?m not sure this is really possible though? many thanks in advance for your answer all the best Massi -------------- next part -------------- An HTML attachment was scrubbed... URL: From Irina.Ilyushkina at vuw.ac.nz Thu Feb 26 07:02:02 2015 From: Irina.Ilyushkina at vuw.ac.nz (Irina Ilyushkina) Date: Thu, 26 Feb 2015 06:02:02 +0000 Subject: [adegenet-forum] scatter plot problem In-Reply-To: References: <2CB2DA8E426F3541AB1907F98ABA6570ABEE3488@icexch-m1.ic.ac.uk> <2CB2DA8E426F3541AB1907F98ABA6570ABEE5A17@icexch-m1.ic.ac.uk>, Message-ID: Thank you very much! Irina Ilyushkina PhD Candidate School of Biological Sciences Victoria University of Wellington P O Box 600 Wellington 6140 New Zealand Mobile: 0223898085 Tel: 04 463 5233 Ext 8135 ________________________________ From: Maria del Carmen David [maria.david.salas at gmail.com] Sent: Thursday, 26 February 2015 1:43 a.m. To: Jombart, Thibaut Cc: Irina Ilyushkina; adegenet-forum at lists.r-forge.r-project.org Subject: Re: [adegenet-forum] scatter plot problem Hi, Irina. Back in September I had a similar question. Caitlin Collins wrote some codes to label individuals. If might be what you were looking for. Message from Caitlin Collins: If you think the individuals you are plotting are spaced far enough that you will be able to read labels at the individual level, one way to do it is to use s.label. Here is an example of how to use s.label to overlap labels to a scatterplot of DAPC: ############# ## EXAMPLE ## ############# set.seed(14) # generate a simulated dataset with 3 populations simpop <- glSim(100, 500, 5, k=3, sort.pop=TRUE) # isolate the SNPs and the population factor snps <- as.matrix(simpop) phen <- simpop at other$ancestral.pops # run a dapc dapc1 <- dapc(snps, phen, n.pca=20, n.da=4) # create the scatter plot as before scatter(dapc1, cstar=0, cex=5, label=NULL) # change graphical parameter to subsequently overlay the labels without drawing a new plot par(new=TRUE) # make a data frame of the dapc coordinates used in scatter df <- data.frame(x = dapc1$ind.coord[,1], y = dapc1$ind.coord[,2]) # identify/ create a vector of names for the individuals in your plot noms <- paste("ind", c(1:100), sep=".") # use the text function to add labels to the positions given by the coordinates you used in plot s.label(dfxy = df, xax=1, yax=2, label=noms, clabel=0.7, # change the size of the labels boxes=TRUE, # if points are spaced wide enough, can use TRUE to add boxes around the labels grid=FALSE, addaxes=FALSE) # do not draw lines or axes in addition to the labels On Wed, Feb 25, 2015 at 5:53 AM, Jombart, Thibaut > wrote: Hello, so I had understood the question, and given you the answer - use the 'pop' argument in ?scatter.dapc. Cheers Thibaut ________________________________ From: Irina Ilyushkina [Irina.Ilyushkina at vuw.ac.nz] Sent: 24 February 2015 22:42 To: Jombart, Thibaut Subject: RE: scatter plot problem I'm sorry for double posting but I'm afraid my Outlook might have failed to include the images in the e-mail. Hi, Thank you very much for the reply! I'm sorry I didn't explain everything clearer. Initially I have 2 populations and they form 3 clusters in DAPC, here is the scatterplot I get with command "scatter(dapc_data, posi.da="bottomleft", bg="white", pch=17:22, scree.da=FALSE, col=myCol)" [cid:7fbe74d8-9d03-420b-a8dd-d913fb75500c] the assignment to the clusters didn't match my population structure perfectly so I need to indicate the origin (which one of 2 initial populations) of each individual in the clusters. I made 2 plots manually in Photoshop to represent my idea better: [cid:859dc59a-2be3-4fa9-8b39-08413fa5b536] or an easier to read color representation: [cid:fddf3b1d-c165-41a8-86b0-b374fab1d57f] Many thanks, Irina Irina Ilyushkina PhD Candidate School of Biological Sciences Victoria University of Wellington P O Box 600 Wellington 6140 New Zealand Mobile: 0223898085 Tel: 04 463 5233 Ext 8135 ________________________________ From: Jombart, Thibaut [t.jombart at imperial.ac.uk] Sent: Tuesday, 24 February 2015 12:58 a.m. To: Irina Ilyushkina; adegenet-forum at lists.r-forge.r-project.org Subject: RE: scatter plot problem Hi Irina, I am not sure I understand what you are after, so sorry if I miss the point. If you want to represent a different group to the one used in the DAPC analysis on the DAPC scatterplot, use the argument 'grp'; from ?scatter.dapc: grp: a factor defining group membership for the individuals. The scatterplot is optimal only for the default group, i.e. the one used in the DAPC analysis. Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Irina Ilyushkina [Irina.Ilyushkina at vuw.ac.nz] Sent: 23 February 2015 04:41 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] scatter plot problem Hi, I'm new to R and would be extremely grateful if someone could help me with my problem. I need to indicate (with labels, with color, etc.) the original group assignment of every individual in the DAPC inferred clusters on the scatter plot. table.value(table(pop(x), grp$grp) is showing the type of plot I'm after but it's a bit confusing when you have to consider two plots at the same time so I'm looking for a way to combine both in one plot if it is possible. Many thanks, Irina _______________________________________________ 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 -- Maria del Carmen David Salas -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Rplotcolors.jpg Type: image/jpeg Size: 40201 bytes Desc: Rplotcolors.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Rpotlabels.jpg Type: image/jpeg Size: 44019 bytes Desc: Rpotlabels.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pomap2_opt1_nooutl_scatter20.jpeg Type: image/jpeg Size: 163399 bytes Desc: pomap2_opt1_nooutl_scatter20.jpeg URL: From emmanuel.wicker at cirad.fr Thu Feb 26 15:38:40 2015 From: emmanuel.wicker at cirad.fr (Emmanuel WICKER) Date: Thu, 26 Feb 2015 18:38:40 +0400 Subject: [adegenet-forum] Help : DAPC and Supplementary individuals In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA6570ABEE5AE1@icexch-m1.ic.ac.uk> References: <54EC5864.4080204@cirad.fr> <2CB2DA8E426F3541AB1907F98ABA6570ABEE5AE1@icexch-m1.ic.ac.uk> Message-ID: <54EF2FF0.9010807@cirad.fr> Thank you Thibaut, I will test that. Cheers Manu Le 25/02/2015 17:02, Jombart, Thibaut a ?crit : > > Hi there, > > the variables are alleles here, not only markers. To ensure that your > datasets have the same alleles, use the function repool to merge the > two datasets, run the DAPC on the chosen subset, and then use the rest > as supplementary individuals. > > Makes sense? > > Cheers > Thibaut > > > ------------------------------------------------------------------------ > *From:* adegenet-forum-bounces at lists.r-forge.r-project.org > [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of > Emmanuel WICKER [emmanuel.wicker at cirad.fr] > *Sent:* 24 February 2015 10:54 > *To:* adegenet-forum at lists.r-forge.r-project.org > *Subject:* [adegenet-forum] Help : DAPC and Supplementary individuals > > Dear all, > I first performed a DAPC on a worlwide dataset genotyped using 8 > microsat loci. Then I tried to inject in this analysis supplementary > individuals , genotyped with all same 8 loci. The error message says > that "the number of variables does not match original data". The loci > are the same in both datasets, can anyone help me find what is going > wrong ? > Cheers > Manu > -- > *Emmanuel WICKER*, PhD > Phytopathologiste / Plant Pathologist > /CIRAD, UMR Peuplements V??g??taux et Bioagresseurs en Milieu Tropical > (PVBMT)/ > P??le de Protection des Plantes > 7, chemin de l'IRAT > F-97410 Saint Pierre > La R??union, France > wicker at cirad.fr > SITE WEB PVBMT > *Tel* : +262 (0) 262 49 92 42 > *Fax* : +262 (0) 262 49 92 93 -- *Emmanuel WICKER*, PhD Phytopathologiste / Plant Pathologist /CIRAD, UMR Peuplements V?g?taux et Bioagresseurs en Milieu Tropical (PVBMT)/ P?le de Protection des Plantes 7, chemin de l'IRAT F-97410 Saint Pierre La R?union, France wicker at cirad.fr SITE WEB PVBMT *Tel* : +262 (0) 262 49 92 42 *Fax* : +262 (0) 262 49 92 93 -------------- next part -------------- An HTML attachment was scrubbed... URL: