From creeb at stanford.edu Fri Aug 4 00:14:01 2017 From: creeb at stanford.edu (Carol Ann Reeb) Date: Thu, 3 Aug 2017 22:14:01 +0000 Subject: [adegenet-forum] Jitter & sPCA Message-ID: I'm having trouble jittering x-coordinates in order to run sPCA. I'm still learning R so I don't know what code would work in adegent. I did find R usage: Jitter(x, factor=1, amount=NULL). But that does not tell me how to call the proper files. I did find code from a supplement from a manuscript comparing MENE to sPCA comparison. And although that routine ran, the program would still not allow me to choose a network to plot sPCA coordinates because it said they were still identical in the xy file. Any help, suggestions would be greatly appreciated. Carol -------------- next part -------------- An HTML attachment was scrubbed... URL: From roman.lustrik at biolitika.si Fri Aug 4 00:53:13 2017 From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=) Date: Fri, 4 Aug 2017 00:53:13 +0200 (CEST) Subject: [adegenet-forum] Jitter & sPCA In-Reply-To: References: Message-ID: <1984498114.46284.1501800793052.JavaMail.zimbra@biolitika.si> As the error is reporting, you should use jitter() on your coordinates. Either specify new jittered coordinates directly to xy argument of spca(), or, jitter your genind object which you can access using `other(x)$xy`. Here's an example of the former approach: > library(adegenet) > data(spcaIllus) > x <- spcaIllus[[1]] > out <- spca(x, ask = FALSE, type = 1, scannf = FALSE) > xy <- other(x)$xy > newxy <- xy[rep(1:(nrow(xy)/10), length.out = nrow(xy)), ] > out.clumped <- spca(x, ask = FALSE, type = 1, scannf = FALSE, xy = newxy) Error in chooseCN(xy = xy, ask = ask, type = type, plot.nb = plot.nb, : Duplicate locations detected and incompatible with graph type 1-4. Please choose another graph (5-7) or add random noise to locations (see ?jitter). > out.jittered <- spca(x, ask = FALSE, type = 1, scannf = FALSE, xy = jitter(newxy)) > Cheers, Roman ---- In god we trust, all others bring data. > Zahtevaj IJZ na https://kurc.biolitika.si From: "Carol Ann Reeb" To: adegenet-forum at lists.r-forge.r-project.org Sent: Friday, August 4, 2017 12:14:01 AM Subject: [adegenet-forum] Jitter & sPCA I'm having trouble jittering x-coordinates in order to run sPCA. I'm still learning R so I don't know what code would work in adegent. I did find R usage: Jitter(x, factor=1, amount=NULL). But that does not tell me how to call the proper files. I did find code from a supplement from a manuscript comparing MENE to sPCA comparison. And although that routine ran, the program would still not allow me to choose a network to plot sPCA coordinates because it said they were still identical in the xy file. Any help, suggestions would be greatly appreciated. Carol _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From thibautjombart at gmail.com Fri Aug 4 15:10:44 2017 From: thibautjombart at gmail.com (Thibaut Jombart) Date: Fri, 4 Aug 2017 14:10:44 +0100 Subject: [adegenet-forum] Fwd: Individuals for genind not plotting dapc In-Reply-To: References:

Message-ID: Dear Philip, it looks like all individuals from a given cluster are exactly at the same location, which would be the case if they are identical genotypes. Assuming your genind object is 'x', can you check what this returns: table(table(apply(genind2df(x, sep="", usepop = FALSE), 1, paste, collapse = ""))) This will derive the frequencies of haplotypes in the data. I think there is something to do this more elegantly in poppr but I will let Zhian comment if this is the case. Best Thibaut -- Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology, Imperial College London Head of RECON: repidemicsconsortium.org WHO Consultant - outbreak analysis sites.google.com/site/thibautjombart/ Twitter: @TeebzR +44(0)20 7594 3658 On 22 July 2017 at 05:19, Phillip Skipwith wrote: > Hi, > > I'm pretty new to Adegenet, but I have been through the tutorials and have > been more or less successful getting it to work on my empirical data. This > is a phylogenomic dataset of 83 individuals from eight clades and 4,268 > loci (I'm using 4,035 SNPs for ordination, etc.). I realize the sample > size is small, but this is hard-earned field data. The problem arises when > I'm trying to use dapc after find.clusters on the below genind object. > > gen.struct > /// GENIND OBJECT ///////// > > // 83 individuals; 4,035 loci; 8,341 alleles; size: 4.5 Mb > > // Basic content > @tab: 83 x 8341 matrix of allele counts > @loc.n.all: number of alleles per locus (range: 2-4) > @loc.fac: locus factor for the 8341 columns of @tab > @all.names: list of allele names for each locus > @ploidy: ploidy of each individual (range: 2-2) > @type: codom > @call: read.structure(file = "final_Struct_good_maybe.str", n.ind = 83, > n.loc = 4035, onerowperind = F, col.lab = 1, col.pop = 2, > row.marknames = 0, ask = F) > > // Optional content > @pop: population of each individual (group size range: 2-27) > > grp <- find.clusters(gen.struct, max.n.clust=35) > > Choose the number PCs to retain (>=1): > 80 > Choose the number of clusters (>=2: > 9 > > dapc1 <- dapc(gen.struct, grp$grp) > > dapc1 > ################################################# > # Discriminant Analysis of Principal Components # > ################################################# > class: dapc > $call: dapc.genind(x = gen.struct, pop = grp$grp) > > $n.pca: 60 first PCs of PCA used > $n.da: 4 discriminant functions saved > $var (proportion of conserved variance): 0.946 > > $eig (eigenvalues): 182000 71010 34130 20710 16790 ... > > vector length content > 1 $eig 8 eigenvalues > 2 $grp 83 prior group assignment > 3 $prior 9 prior group probabilities > 4 $assign 83 posterior group assignment > 5 $pca.cent 8341 centring vector of PCA > 6 $pca.norm 8341 scaling vector of PCA > 7 $pca.eig 82 eigenvalues of PCA > > data.frame nrow ncol content > 1 $tab 83 60 retained PCs of PCA > 2 $means 9 60 group means > 3 $loadings 60 4 loadings of variables > 4 $ind.coord 83 4 coordinates of individuals (principal components) > 5 $grp.coord 9 4 coordinates of groups > 6 $posterior 83 9 posterior membership probabilities > 7 $pca.loadings 8341 60 PCA loadings of original variables > 8 $var.contr 8341 4 contribution of original variables > > Choose the number PCs to retain (>=1): > 60 > Choose the number discriminant functions to retain (>=1): > 4 > > scatter(dapc1, scree.da = T) > > The end result is a plot with the centroid points for each of the clusters > but not the individuals. I know there is probably something simple that I'm > missing or there's something intrinsically wrong with my code and or data. > I've perused the forum for similar issues and nothing is quite spot on to > what I'm asking here. > > Any help would be greatly appreciated. > > Best, > > Phillip > > > > _______________________________________________ > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From thibautjombart at gmail.com Fri Aug 4 15:14:29 2017 From: thibautjombart at gmail.com (Thibaut Jombart) Date: Fri, 4 Aug 2017 14:14:29 +0100 Subject: [adegenet-forum] Jitter & sPCA In-Reply-To: <1984498114.46284.1501800793052.JavaMail.zimbra@biolitika.si> References: <1984498114.46284.1501800793052.JavaMail.zimbra@biolitika.si> Message-ID: Hi Carol, Roman's solution should have worked, but adding random noise to locations may not be ideal anyway. You may prefer using a connection network which can accommodate duplicated locations, such as neighbourhood defined by distance interval (see ?chooseCN). Best Thibaut -- Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology, Imperial College London Head of RECON: repidemicsconsortium.org WHO Consultant - outbreak analysis sites.google.com/site/thibautjombart/ Twitter: @TeebzR +44(0)20 7594 3658 On 3 August 2017 at 23:53, Roman Lu?trik wrote: > As the error is reporting, you should use jitter() on your coordinates. > Either specify new jittered coordinates directly to xy argument of spca(), > or, jitter your genind object which you can access using `other(x)$xy`. > > Here's an example of the former approach: > > > library(adegenet) > > data(spcaIllus) > > x <- spcaIllus[[1]] > > out <- spca(x, ask = FALSE, type = 1, scannf = FALSE) > > xy <- other(x)$xy > > newxy <- xy[rep(1:(nrow(xy)/10), length.out = nrow(xy)), ] > > out.clumped <- spca(x, ask = FALSE, type = 1, scannf = FALSE, xy = newxy) > Error in chooseCN(xy = xy, ask = ask, type = type, plot.nb = plot.nb, : > Duplicate locations detected and incompatible with graph type 1-4. > Please choose another graph (5-7) or add random noise to locations (see > ?jitter). > > out.jittered <- spca(x, ask = FALSE, type = 1, scannf = FALSE, xy = > jitter(newxy)) > > > > Cheers, > Roman > > ---- > In god we trust, all others bring data. > > Zahtevaj IJZ na https://kurc.biolitika.si > > ------------------------------ > *From: *"Carol Ann Reeb" > *To: *adegenet-forum at lists.r-forge.r-project.org > *Sent: *Friday, August 4, 2017 12:14:01 AM > *Subject: *[adegenet-forum] Jitter & sPCA > > I'm having trouble jittering x-coordinates in order to run sPCA. I'm > still learning R so I don't know what code would work in adegent. I did > find R usage: Jitter(x, factor=1, amount=NULL). But that does not tell me > how to call the proper files. I did find code from a supplement from a > manuscript comparing MENE to sPCA comparison. And although that routine > ran, the program would still not allow me to choose a network to plot > sPCA coordinates because it said they were still identical in the xy file. > Any help, suggestions would be greatly appreciated. > > > Carol > > _______________________________________________ > 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 > > _______________________________________________ > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zkamvar at gmail.com Fri Aug 4 18:22:55 2017 From: zkamvar at gmail.com (Zhian Kamvar) Date: Fri, 4 Aug 2017 11:22:55 -0500 Subject: [adegenet-forum] Fwd: Individuals for genind not plotting dapc In-Reply-To: References:

Message-ID: <23E78F34-9A5C-4A7E-B50C-E63BA9AFDF06@gmail.com> Hi Phillip, I would agree with Thibaut to first check to make sure you don't have duplicated genotypes for each cluster in your data. If you use the poppr package, you can use nmll() to check the number of unique genotypes and mll() to view their assignment. One thing I notice in your DAPC output is the fact that you are retaining ~95% of the variance for these artificial groups, which may suggest that you are over-fitting the model (although, I would defer to Thibaut for confirmation on this). This could result in minute differences within the groups as compared to between groups, giving the appearance of all within group points stacked on top of one another if the differences between groups is sufficiently large. My suggestion is to try reducing the number of retained PCs for the DAPC. Sent from my iPhone > On Aug 4, 2017, at 08:10, Thibaut Jombart wrote: > > Dear Philip, > > it looks like all individuals from a given cluster are exactly at the same location, which would be the case if they are identical genotypes. > > Assuming your genind object is 'x', can you check what this returns: > > table(table(apply(genind2df(x, sep="", usepop = FALSE), 1, paste, collapse = ""))) > > This will derive the frequencies of haplotypes in the data. I think there is something to do this more elegantly in poppr but I will let Zhian comment if this is the case. > > Best > Thibaut > > > > > -- > Dr Thibaut Jombart > Lecturer, Department of Infectious Disease Epidemiology, Imperial College London > Head of RECON: repidemicsconsortium.org > WHO Consultant - outbreak analysis > sites.google.com/site/thibautjombart/ > Twitter: @TeebzR > +44(0)20 7594 3658 > >> On 22 July 2017 at 05:19, Phillip Skipwith wrote: >> Hi, >> >> I'm pretty new to Adegenet, but I have been through the tutorials and have been more or less successful getting it to work on my empirical data. This is a phylogenomic dataset of 83 individuals from eight clades and 4,268 loci (I'm using 4,035 SNPs for ordination, etc.). I realize the sample size is small, but this is hard-earned field data. The problem arises when I'm trying to use dapc after find.clusters on the below genind object. >> >> gen.struct >> /// GENIND OBJECT ///////// >> >> // 83 individuals; 4,035 loci; 8,341 alleles; size: 4.5 Mb >> >> // Basic content >> @tab: 83 x 8341 matrix of allele counts >> @loc.n.all: number of alleles per locus (range: 2-4) >> @loc.fac: locus factor for the 8341 columns of @tab >> @all.names: list of allele names for each locus >> @ploidy: ploidy of each individual (range: 2-2) >> @type: codom >> @call: read.structure(file = "final_Struct_good_maybe.str", n.ind = 83, >> n.loc = 4035, onerowperind = F, col.lab = 1, col.pop = 2, >> row.marknames = 0, ask = F) >> >> // Optional content >> @pop: population of each individual (group size range: 2-27) >> >> grp <- find.clusters(gen.struct, max.n.clust=35) >> >> Choose the number PCs to retain (>=1): >> 80 >> Choose the number of clusters (>=2: >> 9 >> >> dapc1 <- dapc(gen.struct, grp$grp) >> >> dapc1 >> ################################################# >> # Discriminant Analysis of Principal Components # >> ################################################# >> class: dapc >> $call: dapc.genind(x = gen.struct, pop = grp$grp) >> >> $n.pca: 60 first PCs of PCA used >> $n.da: 4 discriminant functions saved >> $var (proportion of conserved variance): 0.946 >> >> $eig (eigenvalues): 182000 71010 34130 20710 16790 ... >> >> vector length content >> 1 $eig 8 eigenvalues >> 2 $grp 83 prior group assignment >> 3 $prior 9 prior group probabilities >> 4 $assign 83 posterior group assignment >> 5 $pca.cent 8341 centring vector of PCA >> 6 $pca.norm 8341 scaling vector of PCA >> 7 $pca.eig 82 eigenvalues of PCA >> >> data.frame nrow ncol content >> 1 $tab 83 60 retained PCs of PCA >> 2 $means 9 60 group means >> 3 $loadings 60 4 loadings of variables >> 4 $ind.coord 83 4 coordinates of individuals (principal components) >> 5 $grp.coord 9 4 coordinates of groups >> 6 $posterior 83 9 posterior membership probabilities >> 7 $pca.loadings 8341 60 PCA loadings of original variables >> 8 $var.contr 8341 4 contribution of original variables >> >> Choose the number PCs to retain (>=1): >> 60 >> Choose the number discriminant functions to retain (>=1): >> 4 >> >> scatter(dapc1, scree.da = T) >> >> The end result is a plot with the centroid points for each of the clusters but not the individuals. I know there is probably something simple that I'm missing or there's something intrinsically wrong with my code and or data. I've perused the forum for similar issues and nothing is quite spot on to what I'm asking here. >> >> Any help would be greatly appreciated. >> >> Best, >> >> Phillip >> >> >> >> _______________________________________________ >> 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From thibautjombart at gmail.com Fri Aug 4 22:53:59 2017 From: thibautjombart at gmail.com (Thibaut Jombart) Date: Fri, 4 Aug 2017 21:53:59 +0100 Subject: [adegenet-forum] Fwd: Individuals for genind not plotting dapc In-Reply-To: <23E78F34-9A5C-4A7E-B50C-E63BA9AFDF06@gmail.com> References:

<23E78F34-9A5C-4A7E-B50C-E63BA9AFDF06@gmail.com> Message-ID: Yes I overlooked that, but +1 to Zhian's suggestions. Also a sign I need to get more familiar with poppr ;) Best Thibaut -- Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology, Imperial College London Head of RECON: repidemicsconsortium.org WHO Consultant - outbreak analysis sites.google.com/site/thibautjombart/ Twitter: @TeebzR +44(0)20 7594 3658 On 4 August 2017 at 17:22, Zhian Kamvar wrote: > Hi Phillip, > > I would agree with Thibaut to first check to make sure you don't have > duplicated genotypes for each cluster in your data. If you use the poppr > package, you can use nmll() to check the number of unique genotypes and > mll() to view their assignment. > > One thing I notice in your DAPC output is the fact that you are retaining > ~95% of the variance for these artificial groups, which may suggest that > you are over-fitting the model (although, I would defer to Thibaut for > confirmation on this). This could result in minute differences within the > groups as compared to between groups, giving the appearance of all within > group points stacked on top of one another if the differences between > groups is sufficiently large. > > My suggestion is to try reducing the number of retained PCs for the DAPC. > > Sent from my iPhone > > On Aug 4, 2017, at 08:10, Thibaut Jombart > wrote: > > Dear Philip, > > it looks like all individuals from a given cluster are exactly at the same > location, which would be the case if they are identical genotypes. > > Assuming your genind object is 'x', can you check what this returns: > > table(table(apply(genind2df(x, sep="", usepop = FALSE), 1, paste, > collapse = ""))) > > This will derive the frequencies of haplotypes in the data. I think there > is something to do this more elegantly in poppr but I will let Zhian > comment if this is the case. > > Best > Thibaut > > > > > -- > Dr Thibaut Jombart > Lecturer, Department of Infectious Disease Epidemiology, Imperial College > London > Head of RECON: repidemicsconsortium.org > WHO Consultant - outbreak analysis > sites.google.com/site/thibautjombart/ > Twitter: @TeebzR > +44(0)20 7594 3658 <+44%2020%207594%203658> > > On 22 July 2017 at 05:19, Phillip Skipwith wrote: > >> Hi, >> >> I'm pretty new to Adegenet, but I have been through the tutorials and >> have been more or less successful getting it to work on my empirical data. >> This is a phylogenomic dataset of 83 individuals from eight clades and >> 4,268 loci (I'm using 4,035 SNPs for ordination, etc.). I realize the >> sample size is small, but this is hard-earned field data. The problem >> arises when I'm trying to use dapc after find.clusters on the below genind >> object. >> >> gen.struct >> /// GENIND OBJECT ///////// >> >> // 83 individuals; 4,035 loci; 8,341 alleles; size: 4.5 Mb >> >> // Basic content >> @tab: 83 x 8341 matrix of allele counts >> @loc.n.all: number of alleles per locus (range: 2-4) >> @loc.fac: locus factor for the 8341 columns of @tab >> @all.names: list of allele names for each locus >> @ploidy: ploidy of each individual (range: 2-2) >> @type: codom >> @call: read.structure(file = "final_Struct_good_maybe.str", n.ind = >> 83, >> n.loc = 4035, onerowperind = F, col.lab = 1, col.pop = 2, >> row.marknames = 0, ask = F) >> >> // Optional content >> @pop: population of each individual (group size range: 2-27) >> >> grp <- find.clusters(gen.struct, max.n.clust=35) >> >> Choose the number PCs to retain (>=1): >> 80 >> Choose the number of clusters (>=2: >> 9 >> >> dapc1 <- dapc(gen.struct, grp$grp) >> >> dapc1 >> ################################################# >> # Discriminant Analysis of Principal Components # >> ################################################# >> class: dapc >> $call: dapc.genind(x = gen.struct, pop = grp$grp) >> >> $n.pca: 60 first PCs of PCA used >> $n.da: 4 discriminant functions saved >> $var (proportion of conserved variance): 0.946 >> >> $eig (eigenvalues): 182000 71010 34130 20710 16790 ... >> >> vector length content >> 1 $eig 8 eigenvalues >> 2 $grp 83 prior group assignment >> 3 $prior 9 prior group probabilities >> 4 $assign 83 posterior group assignment >> 5 $pca.cent 8341 centring vector of PCA >> 6 $pca.norm 8341 scaling vector of PCA >> 7 $pca.eig 82 eigenvalues of PCA >> >> data.frame nrow ncol content >> >> 1 $tab 83 60 retained PCs of PCA >> >> 2 $means 9 60 group means >> >> 3 $loadings 60 4 loadings of variables >> >> 4 $ind.coord 83 4 coordinates of individuals (principal >> components) >> 5 $grp.coord 9 4 coordinates of groups >> >> 6 $posterior 83 9 posterior membership probabilities >> >> 7 $pca.loadings 8341 60 PCA loadings of original variables >> >> 8 $var.contr 8341 4 contribution of original variables >> >> Choose the number PCs to retain (>=1): >> 60 >> Choose the number discriminant functions to retain (>=1): >> 4 >> >> scatter(dapc1, scree.da = T) >> >> The end result is a plot with the centroid points for each of the >> clusters but not the individuals. I know there is probably something simple >> that I'm missing or there's something intrinsically wrong with my code and >> or data. I've perused the forum for similar issues and nothing is quite >> spot on to what I'm asking here. >> >> Any help would be greatly appreciated. >> >> Best, >> >> Phillip >> >> >> >> _______________________________________________ >> 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 >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arsalan at pobox.com Thu Aug 24 21:22:48 2017 From: arsalan at pobox.com (Arsalan Emami-Khoyi) Date: Thu, 24 Aug 2017 21:22:48 +0200 Subject: [adegenet-forum] IBD distance matrices Message-ID: <1503602568.3829240.1084057312.5F6F3209@webmail.messagingengine.com> Dear Thibut and Adegenet team, I would like to thank you for your contributions to the scientific community.I am estimating IBD for the same species using three different data sets : mtDNA,microsatellie, and SNPs.For being consistent across the data sets we need to use appropriate distance matrices.I am wondering if there is any way to use our in-house distant matrices instead of provided distance measures?I will deeply appreciate your suggestions regarding the optimal distant method for each kind of data sets.Many thanks in advance and see you in October! Regards Arsalan Emami-Khoyi Postdoctoral Research Fellow in Wildlife Genomics University of Johannesburg_Center for Ecological Genomics and Wildlife ConservationAuckland Park 2006 South Africa Email : Arsalane at uj.ac.za Phone :+27 (0)11 559 3373 Cellphone:+27 79 88 14 628 Website :https://sites.google.com/site/drpeterteske/postdocs -------------- next part -------------- An HTML attachment was scrubbed... URL: From thibautjombart at gmail.com Fri Aug 25 13:23:03 2017 From: thibautjombart at gmail.com (Thibaut Jombart) Date: Fri, 25 Aug 2017 12:23:03 +0100 Subject: [adegenet-forum] IBD distance matrices In-Reply-To: <1503602568.3829240.1084057312.5F6F3209@webmail.messagingengine.com> References: <1503602568.3829240.1084057312.5F6F3209@webmail.messagingengine.com> Message-ID: Hi there, yes, you can provide whatever 'dist' object you want to ade4::mantel.randtest. If you start from a symmetric matrix coming from another software, you can read it into R and convert it to dist using 'as.dist'. Cheers Thibaut -- Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology, Imperial College London Head of RECON: repidemicsconsortium.org WHO Consultant - outbreak analysis sites.google.com/site/thibautjombart/ Twitter: @TeebzR +44(0)20 7594 3658 On 24 August 2017 at 20:22, Arsalan Emami-Khoyi wrote: > Dear Thibut and Adegenet team, > I would like to thank you for your contributions to the scientific > community. > I am estimating IBD for the same species using three different data sets > : mtDNA,microsatellie, and SNPs. > For being consistent across the data sets we need to use appropriate > distance matrices. > I am wondering if there is any way to use our in-house distant matrices > instead of provided distance measures? > I will deeply appreciate your suggestions regarding the optimal distant > method for each kind of data sets. > Many thanks in advance and see you in October! > > > > Regards > > Arsalan Emami-Khoyi > Postdoctoral Research Fellow in Wildlife Genomics > University of Johannesburg_Center for Ecological Genomics and Wildlife > Conservation > Auckland Park 2006 > South Africa > Email : Arsalane at uj.ac.za > Phone :+27 (0)11 559 3373 <+27%2011%20559%203373> > Cellphone:+27 79 88 14 628 > Website :https://sites.google.com/site/drpeterteske/postdocs > > > _______________________________________________ > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arsalan at pobox.com Fri Aug 25 14:54:54 2017 From: arsalan at pobox.com (Arsalan Emami-Khoyi) Date: Fri, 25 Aug 2017 14:54:54 +0200 Subject: [adegenet-forum] IBD distance matrices In-Reply-To: References: <1503602568.3829240.1084057312.5F6F3209@webmail.messagingengine.com> Message-ID: <1503665694.3640301.1084812696.458FCA3E@webmail.messagingengine.com> Dear Thibuat, Many thanks for your kind email.Looking forward to see you in October. Regards Arsalan Emami-Khoyi Postdoctoral Research Fellow in Wildlife Genomics University of Johannesburg_Center for Ecological Genomics and Wildlife ConservationAuckland Park 2006 South Africa Email : Arsalane at uj.ac.za Phone :+27 (0)11 559 3373 Cellphone:+27 79 88 14 628 Website :https://sites.google.com/site/drpeterteske/postdocs On Fri, Aug 25, 2017, at 01:23 PM, Thibaut Jombart wrote: > Hi there, > > yes, you can provide whatever 'dist' object you want to > ade4::mantel.randtest. If you start from a symmetric matrix coming > from another software, you can read it into R and convert it to dist > using 'as.dist'.> > Cheers > Thibaut > > > -- > Dr Thibaut Jombart > Lecturer, Department of Infectious Disease Epidemiology, Imperial > College London> Head of RECON: repidemicsconsortium.org > WHO Consultant - outbreak analysis > sites.google.com/site/thibautjombart/ > Twitter: @TeebzR > +44(0)20 7594 3658 > > On 24 August 2017 at 20:22, Arsalan Emami-Khoyi > wrote:>> __ >> Dear Thibut and Adegenet team, >> I would like to thank you for your contributions to the scientific >> community.>> I am estimating IBD for the same species using three different data >> sets : mtDNA,microsatellie, and SNPs.>> For being consistent across the data sets we need to use appropriate >> distance matrices.>> I am wondering if there is any way to use our in-house distant >> matrices instead of provided distance measures?>> I will deeply appreciate your suggestions regarding the optimal >> distant method for each kind of data sets.>> Many thanks in advance and see you in October! >> >> >> >> Regards >> >> Arsalan Emami-Khoyi >> Postdoctoral Research Fellow in Wildlife Genomics >> University of Johannesburg_Center for Ecological Genomics and >> Wildlife Conservation>> Auckland Park 2006 >> South Africa >> Email : Arsalane at uj.ac.za >> Phone :+27 (0)11 559 3373[1] >> Cellphone:+27 79 88 14 628 >> Website :https://sites.google.com/site/drpeterteske/postdocs >> >> >> _______________________________________________ >> 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 Links: 1. tel:+27%2011%20559%203373 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Landivincenzo at yahoo.it Sat Aug 26 22:06:29 2017 From: Landivincenzo at yahoo.it (Vincenzo Landi, PhD) Date: Sat, 26 Aug 2017 22:06:29 +0200 Subject: [adegenet-forum] save image for publication Message-ID: <0b212714-b622-2bc8-b789-518d03a431a5@yahoo.it> Dear all, please anybody know some string to export high resolution image form adegenet plot as Tiff or pdf ? Thnak you -- Vincenzo Landi, PhD Animal Breeding Consulting, S.L. Laboratorio de Gen?tica Molecular Aplicada Empresa de Base Tecnol?gica de la Universidad de C?rdoba Parque Cient?fico Tecnol?gico de C?rdoba c/ Astronoma Cecilia Payne 8?1 Edif. Centauro 14014 C?rdoba (Espa?a) www.abcgenetica.com/ Tf: +34957218708, +34630639439 FAX: +34957218706 From vojta at trapa.cz Sun Aug 27 22:48:30 2017 From: vojta at trapa.cz (=?utf-8?B?Vm9qdMSbY2g=?= Zeisek) Date: Sun, 27 Aug 2017 22:48:30 +0200 Subject: [adegenet-forum] save image for publication In-Reply-To: <0b212714-b622-2bc8-b789-518d03a431a5@yahoo.it> References: <0b212714-b622-2bc8-b789-518d03a431a5@yahoo.it> Message-ID: <2542676.eY1OaJtBTD@tilia> Hello, I'm not sure if I answer in the way You'll like, but I use svg() function to export SVG. It is vector format, where everything is independent graphical object. So that I can easily edit the figure in software like Inkscape and export PNG in any quality. HTH, V. Dne sobota 26. srpna 2017 22:06:29 CEST, Vincenzo Landi, PhD napsal(a): > Dear all, > > please anybody know some string to export high resolution image form > adegenet plot as Tiff or pdf ? > > Thnak you -- Vojt?ch Zeisek https://trapa.cz/ -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: This is a digitally signed message part. URL: From roman.lustrik at biolitika.si Mon Aug 28 09:26:51 2017 From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=) Date: Mon, 28 Aug 2017 09:26:51 +0200 (CEST) Subject: [adegenet-forum] save image for publication In-Reply-To: <0b212714-b622-2bc8-b789-518d03a431a5@yahoo.it> References: <0b212714-b622-2bc8-b789-518d03a431a5@yahoo.it> Message-ID: <1270915070.114327.1503905211726.JavaMail.zimbra@biolitika.si> Does `?pdf` work for you? Cheers, Roman ---- In god we trust, all others bring data. > Zahtevaj IJZ na https://kurc.biolitika.si ----- Original Message ----- From: "Vincenzo Landi, PhD" To: adegenet-forum at lists.r-forge.r-project.org Sent: Saturday, August 26, 2017 10:06:29 PM Subject: [adegenet-forum] save image for publication Dear all, please anybody know some string to export high resolution image form adegenet plot as Tiff or pdf ? Thnak you -- Vincenzo Landi, PhD Animal Breeding Consulting, S.L. Laboratorio de Gen?tica Molecular Aplicada Empresa de Base Tecnol?gica de la Universidad de C?rdoba Parque Cient?fico Tecnol?gico de C?rdoba c/ Astronoma Cecilia Payne 8?1 Edif. Centauro 14014 C?rdoba (Espa?a) www.abcgenetica.com/ Tf: +34957218708, +34630639439 FAX: +34957218706 _______________________________________________ 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 landivincenzo at yahoo.it Mon Aug 28 12:32:07 2017 From: landivincenzo at yahoo.it (Vincenzo Landi) Date: Mon, 28 Aug 2017 07:32:07 -0300 Subject: [adegenet-forum] adegenet-forum Digest, Vol 108, Issue 9 In-Reply-To: References: Message-ID: Dear vojta, thank you for your email , please can you post an example of the svg function ? Than you Enviado desde mi iPhone > El 28 ago 2017, a las 7:00, adegenet-forum-request at lists.r-forge.r-project.org escribi?: > > Send adegenet-forum mailing list submissions to > adegenet-forum at lists.r-forge.r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum > > or, via email, send a message with subject or body 'help' to > adegenet-forum-request at lists.r-forge.r-project.org > > You can reach the person managing the list at > adegenet-forum-owner at lists.r-forge.r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of adegenet-forum digest..." > > > Today's Topics: > > 1. Re: save image for publication (Vojt?ch Zeisek) > 2. Re: save image for publication (Roman Lu?trik) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 27 Aug 2017 22:48:30 +0200 > From: Vojt?ch Zeisek > To: adegenet-forum at lists.r-forge.r-project.org > Subject: Re: [adegenet-forum] save image for publication > Message-ID: <2542676.eY1OaJtBTD at tilia> > Content-Type: text/plain; charset="utf-8" > > Hello, > I'm not sure if I answer in the way You'll like, but I use svg() function to > export SVG. It is vector format, where everything is independent graphical > object. So that I can easily edit the figure in software like Inkscape and > export PNG in any quality. > HTH, > V. > > Dne sobota 26. srpna 2017 22:06:29 CEST, Vincenzo Landi, PhD napsal(a): >> Dear all, >> >> please anybody know some string to export high resolution image form >> adegenet plot as Tiff or pdf ? >> >> Thnak you > -- > Vojt?ch Zeisek > https://trapa.cz/ > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: signature.asc > Type: application/pgp-signature > Size: 833 bytes > Desc: This is a digitally signed message part. > URL: > > ------------------------------ > > Message: 2 > Date: Mon, 28 Aug 2017 09:26:51 +0200 (CEST) > From: Roman Lu?trik > To: "Vincenzo Landi, PhD" > Cc: adegenet-forum at lists.r-forge.r-project.org > Subject: Re: [adegenet-forum] save image for publication > Message-ID: > <1270915070.114327.1503905211726.JavaMail.zimbra at biolitika.si> > Content-Type: text/plain; charset=utf-8 > > Does `?pdf` work for you? > > Cheers, > Roman > > ---- > In god we trust, all others bring data. >> Zahtevaj IJZ na https://kurc.biolitika.si > > ----- Original Message ----- > From: "Vincenzo Landi, PhD" > To: adegenet-forum at lists.r-forge.r-project.org > Sent: Saturday, August 26, 2017 10:06:29 PM > Subject: [adegenet-forum] save image for publication > > Dear all, > > please anybody know some string to export high resolution image form > adegenet plot as Tiff or pdf ? > > Thnak you > > -- > Vincenzo Landi, PhD > Animal Breeding Consulting, S.L. > Laboratorio de Gen?tica Molecular Aplicada > Empresa de Base Tecnol?gica de la Universidad de C?rdoba > Parque Cient?fico Tecnol?gico de C?rdoba > c/ Astronoma Cecilia Payne 8?1 > Edif. Centauro 14014 C?rdoba (Espa?a) > www.abcgenetica.com/ > Tf: +34957218708, +34630639439 > FAX: +34957218706 > > _______________________________________________ > 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 > > > ------------------------------ > > _______________________________________________ > 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 > > End of adegenet-forum Digest, Vol 108, Issue 9 > ********************************************** From landivincenzo at yahoo.it Mon Aug 28 12:41:30 2017 From: landivincenzo at yahoo.it (Vincenzo Landi) Date: Mon, 28 Aug 2017 07:41:30 -0300 Subject: [adegenet-forum] save image for publication In-Reply-To: <1270915070.114327.1503905211726.JavaMail.zimbra@biolitika.si> References: <0b212714-b622-2bc8-b789-518d03a431a5@yahoo.it> <1270915070.114327.1503905211726.JavaMail.zimbra@biolitika.si> Message-ID: <323BF7D5-21B2-473C-A8EF-5E2BA402A901@yahoo.it> Hello, yes PDF if good. Than you Enviado desde mi iPhone > El 28 ago 2017, a las 4:26, Roman Lu?trik escribi?: > > Does `?pdf` work for you? > > Cheers, > Roman > > ---- > In god we trust, all others bring data. >> Zahtevaj IJZ na https://kurc.biolitika.si > > ----- Original Message ----- > From: "Vincenzo Landi, PhD" > To: adegenet-forum at lists.r-forge.r-project.org > Sent: Saturday, August 26, 2017 10:06:29 PM > Subject: [adegenet-forum] save image for publication > > Dear all, > > please anybody know some string to export high resolution image form > adegenet plot as Tiff or pdf ? > > Thnak you > > -- > Vincenzo Landi, PhD > Animal Breeding Consulting, S.L. > Laboratorio de Gen?tica Molecular Aplicada > Empresa de Base Tecnol?gica de la Universidad de C?rdoba > Parque Cient?fico Tecnol?gico de C?rdoba > c/ Astronoma Cecilia Payne 8?1 > Edif. Centauro 14014 C?rdoba (Espa?a) > www.abcgenetica.com/ > Tf: +34957218708, +34630639439 > FAX: +34957218706 > > _______________________________________________ > 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 ramireddyag at gmail.com Mon Aug 28 16:54:02 2017 From: ramireddyag at gmail.com (venkata ramireddy) Date: Mon, 28 Aug 2017 20:24:02 +0530 Subject: [adegenet-forum] thanks giving Message-ID: thanks lot for accepting my request -- Dr. S. V. R. Reddy Ph.D Lead Research support functions LIMAGRAIN, India venkata.sanampudi at limagrain.in Phone 918008019146 From Ngoc-Tien.Tran at insa-rennes.fr Mon Aug 7 14:46:08 2017 From: Ngoc-Tien.Tran at insa-rennes.fr (Ngoc-Tien Tran) Date: Mon, 07 Aug 2017 12:46:08 -0000 Subject: [adegenet-forum] Loci selection for SNP data Message-ID: <160565061.1889947.1502109951577.JavaMail.zimbra@insa-rennes.fr> Hello, I'm working with SNP data with a large number of loci. I would like to know if there is a tool in the package "adegenet" allowing me to select just one smaller set of loci without loosing information. Thanks for your help ! Best wishes, Ngoc-Tien -- -------------------------------------------------------------- TRAN Ngoc-Tien D?partement G?nie Math?matiques/Analyse de Risque et Optimisation et Mod?lisation. INSA-Rennes Tel : +33.(0)7.51.57.96.53 @mail : ngoc-tien.tran at insa-rennes.fr