From maria.david.salas at gmail.com  Wed Mar  1 13:40:24 2017
From: maria.david.salas at gmail.com (Maria del Carmen David)
Date: Wed, 1 Mar 2017 07:40:24 -0500
Subject: [adegenet-forum] scatter plot labels
In-Reply-To: <6773CB2C-48AD-492C-9C78-94096F896BBB@cmich.edu>
References: <6773CB2C-48AD-492C-9C78-94096F896BBB@cmich.edu>
Message-ID: <CAMzhv9rfmcdev61q2CMEONKfb8LBGvTOgaG-LuC-osOKXybZpw@mail.gmail.com>

This must be somewhere in the email records, it's a message from Caitlin
Collins on 2014:

Hi,

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


The comments in the example above hopefully should give you all of the
relevant information, so please give them a read and then feel free to let
me know if you have any questions. You will almost certainly want to play
around with the arguments clabel and boxes in the s.label function to get
the labels to be readable for your case.
I hope that helps!
--------------------------------------
I don't know if it will have the same results now, I mean, in case any
upgrade in the package could have change the function of these commands.
But it worked fine when I used it back then.

On Tue, Feb 28, 2017 at 4:43 PM, Mahon, Andrew R <mahon2a at cmich.edu> wrote:

> Hi all,
> New to using adegenet. Quick question (that may or may not be simple?.).
> Is there a way to use actual sample labels (i.e., what I named them) and
> plotting them in the scatter of the DAPC (i.e., when you run scatter(dapc)
> command)?
>
> Thanks for any help in advance.
>
> -andy
> --
>
>
>
> _______________________________________________
> 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
>
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From fhernandeu at uc.cl  Thu Mar  2 18:04:42 2017
From: fhernandeu at uc.cl (=?UTF-8?Q?Felipe_Hern=C3=A1ndez?=)
Date: Thu, 2 Mar 2017 12:04:42 -0500
Subject: [adegenet-forum] HWE calculation
Message-ID: <CAEGfAaOGc1z7zCn9yAuBAcTQb9jHkKDxXVpU5wePGPU9cfzp+w@mail.gmail.com>

Hi everyone,

I have used the adegenet/pegas packages to estimate HWE using a genind
object. I got the results from chi-squared and exact test based on Monte
Carlo for my whole set of loci (52 loci) across all my 29 populations. I
wonder if there is any option to calculate HWE and get exact test Monte
Carlo results, but for each population separately. Sorry if the question is
so basic, but I would appreciate any helpful advice!

Best,
Felipe

-- 
Felipe Hern?ndez
M?dico Veterinario (DVM), MSc.
PhD. Candidate
Interdisciplinary Ecology Program
School of Natural Resources and Environment
Wildlife Ecology and Conservation Department
University of Florida
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From roman.lustrik at biolitika.si  Fri Mar  3 11:21:55 2017
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Fri, 3 Mar 2017 11:21:55 +0100 (CET)
Subject: [adegenet-forum] HWE calculation
In-Reply-To: <CAEGfAaOGc1z7zCn9yAuBAcTQb9jHkKDxXVpU5wePGPU9cfzp+w@mail.gmail.com>
References: <CAEGfAaOGc1z7zCn9yAuBAcTQb9jHkKDxXVpU5wePGPU9cfzp+w@mail.gmail.com>
Message-ID: <1032246952.496264.1488536515931.JavaMail.zimbra@biolitika.si>

Perhaps something like this? 

library(adegenet) 
library(pegas) 

data(nancycats) 

lvls <- levels(pop(nancycats)) 
out <- vector("list", length(lvls)) # prepare list for output 
names(out) <- lvls 

for (i in lvls) { 
out[[i]] <- hw.test(nancycats[pop(nancycats) == i]) 
} 

Cheers, 
Roman 

---- 
In god we trust, all others bring data. 


From: "Felipe Hern?ndez" <fhernandeu at uc.cl> 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Thursday, March 2, 2017 6:04:42 PM 
Subject: [adegenet-forum] HWE calculation 

Hi everyone, 

I have used the adegenet/pegas packages to estimate HWE using a genind object. I got the results from chi-squared and exact test based on Monte Carlo for my whole set of loci (52 loci) across all my 29 populations. I wonder if there is any option to calculate HWE and get exact test Monte Carlo results, but for each population separately. Sorry if the question is so basic, but I would appreciate any helpful advice! 

Best, 
Felipe 

-- 
Felipe Hern?ndez 
M?dico Veterinario (DVM), MSc. 
PhD. Candidate 
Interdisciplinary Ecology Program 
School of Natural Resources and Environment 
Wildlife Ecology and Conservation Department 
University of Florida 

_______________________________________________ 
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 
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From thibautjombart at gmail.com  Fri Mar  3 12:20:00 2017
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Fri, 3 Mar 2017 11:20:00 +0000
Subject: [adegenet-forum] HWE calculation
In-Reply-To: <1032246952.496264.1488536515931.JavaMail.zimbra@biolitika.si>
References: <CAEGfAaOGc1z7zCn9yAuBAcTQb9jHkKDxXVpU5wePGPU9cfzp+w@mail.gmail.com>
 <1032246952.496264.1488536515931.JavaMail.zimbra@biolitika.si>
Message-ID: <CANPRA+q3A0SMNBefPZ8=JZb3QEEdx6nVKr_HOjqpyvBaGifoKw@mail.gmail.com>

As a side note, Felipe, please avoid posting the same msg to several
mailing lists at the same time, as it makes tracking answers much more
difficult.

Best

Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
sites.google.com/site/thibautjombart/
github.com/thibautjombart
Twitter: @TeebzR <http://twitter.com/TeebzR>
+44(0)20 7594 3658

On 3 March 2017 at 10:21, Roman Lu?trik <roman.lustrik at biolitika.si> wrote:

> Perhaps something like this?
>
> library(adegenet)
> library(pegas)
>
> data(nancycats)
>
> lvls <- levels(pop(nancycats))
> out <- vector("list", length(lvls)) # prepare list for output
> names(out) <- lvls
>
> for (i in lvls) {
>   out[[i]] <- hw.test(nancycats[pop(nancycats) == i])
> }
>
> Cheers,
> Roman
>
> ----
> In god we trust, all others bring data.
>
> ------------------------------
> *From: *"Felipe Hern?ndez" <fhernandeu at uc.cl>
> *To: *adegenet-forum at lists.r-forge.r-project.org
> *Sent: *Thursday, March 2, 2017 6:04:42 PM
> *Subject: *[adegenet-forum] HWE calculation
>
> Hi everyone,
>
> I have used the adegenet/pegas packages to estimate HWE using a genind
> object. I got the results from chi-squared and exact test based on Monte
> Carlo for my whole set of loci (52 loci) across all my 29 populations. I
> wonder if there is any option to calculate HWE and get exact test Monte
> Carlo results, but for each population separately. Sorry if the question is
> so basic, but I would appreciate any helpful advice!
>
> Best,
> Felipe
>
> --
> Felipe Hern?ndez
> M?dico Veterinario (DVM), MSc.
> PhD. Candidate
> Interdisciplinary Ecology Program
> School of Natural Resources and Environment
> Wildlife Ecology and Conservation Department
> University of Florida
>
> _______________________________________________
> 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
>
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From alangarcia87 at hotmail.com  Fri Mar  3 18:18:56 2017
From: alangarcia87 at hotmail.com (Alan Garcia-Elfring)
Date: Fri, 3 Mar 2017 17:18:56 +0000
Subject: [adegenet-forum] DAPC - 3.4 Interpreting variable contributions
 (using a genlight object)
In-Reply-To: <DM5PR22MB0281FA9FC4B733D84003AB06DD570@DM5PR22MB0281.namprd22.prod.outlook.com>
References: <DM5PR22MB0281FA9FC4B733D84003AB06DD570@DM5PR22MB0281.namprd22.prod.outlook.com>
Message-ID: <DM5PR22MB02813B53E4BEB3A5BB09D287DD2B0@DM5PR22MB0281.namprd22.prod.outlook.com>

(2nd try)

Hi all,


I have a genlight object and I would like to analyze the contributions of different alleles to populations structure.


The example on the manual is for genind objects and a previous answer indicated that the fix-around, using as.data.frame, is only good for haploid data. http://lists.r-forge.r-project.org/pipermail/adegenet-forum/2014-May/000840.html

Is it yet possible to do section 3.4 (Jombart and Collins 2015) with a diploid dataset? It would be really cool if so!

Thanks,

Alan

> pldata
 /// GENLIGHT OBJECT /////////

 // 223 genotypes,  76,288 binary SNPs, size: 9 Mb
 0 (0 %) missing data

 // Basic content
   @gen: list of 223 SNPbin
   @ploidy: ploidy of each individual  (range: 2-2)

 // Optional content
   @ind.names:  223 individual labels
   @loc.names:  76288 locus labels
   @pop: population of each individual (group size range: 1-1)
   @other: a list containing: sex  phenotype  pat  mat

> freq399 <- tab(genind2genpop(pldata[loc=c("41837")]),freq=TRUE)
Error in genind2genpop(pldata[loc = c("41837")]) :
  x is not a valid genind object
[cid:732fdd8f-ab46-46ff-97d3-0dd3b4bc8971]




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From S.Bourne at soton.ac.uk  Tue Mar 28 14:02:01 2017
From: S.Bourne at soton.ac.uk (Bourne S.)
Date: Tue, 28 Mar 2017 12:02:01 +0000
Subject: [adegenet-forum] dist.genpop giving NaNs
Message-ID: <AM3PR04MB1507122227C70D9B141D0688D3320@AM3PR04MB1507.eurprd04.prod.outlook.com>

Hi there,


I've got three species I'm looking to do a mantel test on, but for some reason only one of them gives results when calculating the genetic distance between populations with dist.genpop. All three are based off genepops which are generated the same way and in the exact same format. I import them as a genind, then reconvert to genpop to run the dist.genpop on. One of them works fine, the others give NaN, and then do not work when performing the mantel test as NaNs are present.


I'm a bit confused because they're all in the same format, and if one works then all should work.


Has anyone come across this and been able to overcome it?


Cheers,

Steve

---------------------------------------------
Steven Bourne
PhD Student - Adaptation and Genomics of Biological Invasions
School of Ocean and Earth Science
National Oceanography Centre
University of Southampton



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From roman.lustrik at biolitika.si  Tue Mar 28 14:28:40 2017
From: roman.lustrik at biolitika.si (Roman =?utf-8?Q?Lu=C5=A1trik?=)
Date: Tue, 28 Mar 2017 14:28:40 +0200 (CEST)
Subject: [adegenet-forum] dist.genpop giving NaNs
In-Reply-To: <AM3PR04MB1507122227C70D9B141D0688D3320@AM3PR04MB1507.eurprd04.prod.outlook.com>
References: <AM3PR04MB1507122227C70D9B141D0688D3320@AM3PR04MB1507.eurprd04.prod.outlook.com>
Message-ID: <1869061957.37252.1490704120437.JavaMail.zimbra@biolitika.si>

Can you make a reproducible example and post an issue at GitHub? 
https://github.com/thibautjombart/adegenet/issues 

Cheers, 
Roman 

---- 
In god we trust, all others bring data. 


From: "Bourne S." <S.Bourne at soton.ac.uk> 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Tuesday, March 28, 2017 2:02:01 PM 
Subject: [adegenet-forum] dist.genpop giving NaNs 



Hi there, 




I've got three species I'm looking to do a mantel test on, but for some reason only one of them gives results when calculating the genetic distance between populations with dist.genpop. All three are based off genepops which are generated the same way and in the exact same format. I import them as a genind, then reconvert to genpop to run the dist.genpop on. One of them works fine, the others give NaN, and then do not work when performing the mantel test as NaNs are present. 




I'm a bit confused because they're all in the same format, and if one works then all should work. 




Has anyone come across this and been able to overcome it? 




Cheers, 

Steve 
--------------------------------------------- 
Steven Bourne 
PhD Student - Adaptation and Genomics of Biological Invasions 
School of Ocean and Earth Science 
National Oceanography Centre 
University of Southampton 




_______________________________________________ 
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 
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From thibautjombart at gmail.com  Wed Mar 29 14:49:43 2017
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Wed, 29 Mar 2017 13:49:43 +0100
Subject: [adegenet-forum] dist.genpop giving NaNs
In-Reply-To: <1869061957.37252.1490704120437.JavaMail.zimbra@biolitika.si>
References: <AM3PR04MB1507122227C70D9B141D0688D3320@AM3PR04MB1507.eurprd04.prod.outlook.com>
 <1869061957.37252.1490704120437.JavaMail.zimbra@biolitika.si>
Message-ID: <CANPRA+oY3jUc3Rn1QFcpC0DPELs3nZ0jgSbFyx62mXxh2-iNSw@mail.gmail.com>

Hi there,

+1 to a reproducible example.

Usual reasons for this would be missing data in  your allele counts.
Check tab(x) where 'x' is your genpop object to have an idea.

Cheers
Thibaut

--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College London
Head of RECON: repidemicsconsortium.org
sites.google.com/site/thibautjombart/
github.com/thibautjombart
Twitter: @TeebzR
+44(0)20 7594 3658


On 28 March 2017 at 13:28, Roman Lu?trik <roman.lustrik at biolitika.si> wrote:
> Can you make a reproducible example and post an issue at GitHub?
> https://github.com/thibautjombart/adegenet/issues
>
> Cheers,
> Roman
>
> ----
> In god we trust, all others bring data.
>
> ________________________________
> From: "Bourne S." <S.Bourne at soton.ac.uk>
> To: adegenet-forum at lists.r-forge.r-project.org
> Sent: Tuesday, March 28, 2017 2:02:01 PM
> Subject: [adegenet-forum] dist.genpop giving NaNs
>
> Hi there,
>
>
> I've got three species I'm looking to do a mantel test on, but for some
> reason only one of them gives results when calculating the genetic distance
> between populations with dist.genpop. All three are based off genepops which
> are generated the same way and in the exact same format. I import them as a
> genind, then reconvert to genpop to run the dist.genpop on. One of them
> works fine, the others give NaN, and then do not work when performing the
> mantel test as NaNs are present.
>
>
> I'm a bit confused because they're all in the same format, and if one works
> then all should work.
>
>
> Has anyone come across this and been able to overcome it?
>
>
> Cheers,
>
> Steve
>
> ---------------------------------------------
> Steven Bourne
> PhD Student - Adaptation and Genomics of Biological Invasions
> School of Ocean and Earth Science
> National Oceanography Centre
> University of Southampton
>
>
>
>
> _______________________________________________
> 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

From M.Ruhsam at rbge.ac.uk  Mon Mar 20 16:16:26 2017
From: M.Ruhsam at rbge.ac.uk (Markus Ruhsam)
Date: Mon, 20 Mar 2017 15:16:26 +0000
Subject: [adegenet-forum] Older version of adegenet
Message-ID: <6597957BE88F22419CB987B2E084C50504F73E9E502D@MBX-EXC-ED-01.rbge.org.uk>

Hello,

I would like to install v1.4-1 but the link on the http://adegenet.r-forge.r-project.org/ website to the Windows binary results in an 404 error. Has this been moved or is the file not available more?

Thank you

Markus








Dr Markus Ruhsam
Molecular Plant Ecologist
Royal Botanic Garden Edinburgh
20A Inverleith Row
Edinburgh
EH3 5LR
United Kingdom

Tel: +44 (0) 131 248 2859
Fax: +44 (0) 131 248 2901

http://www.rbge.org.uk/science/genetics-and-conservation/markus-ruhsam-homepage

The mission of the Royal Botanic Garden Edinburgh is to "To explore, conserve and explain the world of plants for a better future"


[cid:image001.png at 01D2A18C.F14CA0B0]

The Royal Botanic Garden Edinburgh is a charity registered in Scotland (No SC007983)
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From bowlese at gmail.com  Thu Mar 30 22:27:31 2017
From: bowlese at gmail.com (Ella Bowles)
Date: Thu, 30 Mar 2017 16:27:31 -0400
Subject: [adegenet-forum] addendum to question about how to remove outliers
	(http://lists.r-forge.r-project.org/pipermail/adegenet-forum/2015-July/001194.html)
Message-ID: <CAHpKFdAUaDBGx0gpsHR+StAbMwxwXT-UuLXo7MoAt4ujh7n2_Q@mail.gmail.com>

Hello,

I am trying to remove a set of loci, as in the question posted here:
http://lists.r-forge.r-project.org/pipermail/adegenet-forum/2015-July/001194.html.
However, I'm wondering if there is a way to list the exact locus names
instead of simply the position of the locus. And, what is more, if there is
a way to provide a vector with loci to remove, with the identifier be only
part of the full locus name?

Say I have the following
> dat.s_subset <- dat.s[1:5,1:5]
> dat.s_subset
/// GENIND OBJECT /////////

 // 5 individuals; 3 loci; 5 alleles; size: 6.7 Kb

 // Basic content
   @tab:  5 x 5 matrix of allele counts
   @loc.n.all: number of alleles per locus (range: 1-2)
   @loc.fac: locus factor for the 5 columns of @tab
   @all.names: list of allele names for each locus
   @ploidy: ploidy of each individual  (range: 2-2)
   @type:  codom
   @call: .local(x = x, i = i, j = j, drop = drop)

 // Optional content
   @pop: population of each individual (group size range: 5-5)
> locNames(dat.s_subset)
[1] "12706_10" "14223_16" "14481_7"

As I understand it, if I want to remove locus 14223_16, I can use
> toRemove=c(2)
> x=dat.s_subset[loc=-toRemove]
> x
/// GENIND OBJECT /////////

 // 5 individuals; 2 loci; 3 alleles; size: 6.3 Kb

 // Basic content
   @tab:  5 x 3 matrix of allele counts
   @loc.n.all: number of alleles per locus (range: 1-2)
   @loc.fac: locus factor for the 3 columns of @tab
   @all.names: list of allele names for each locus
   @ploidy: ploidy of each individual  (range: 2-2)
   @type:  codom
   @call: .local(x = x, i = i, j = j, loc = ..1, drop = drop)

 // Optional content
   @pop: population of each individual (group size range: 5-5)
> locNames(x)
[1] "12706_10" "14481_7"

However, I have thousands of loci, and from the analysis that I have done,
my vector of loci that I want to remove has the number of the locus before
the underscore. Is there a way of specifying loci using only this
information? So, I'd need something like the unix wildcard "*", and to be
able to say something like toRemove=c(14223*).

I've done a bunch of searching on the web to see if it would be easier to
do this outside of adegenet, but it seems like it is going to be hard.

Any help would be much appreciated.

Sincerely,
Ella

-- 
Ella Bowles, PhD
Postdoctoral Researcher
Department of Biology
Concordia University

Website: https://ellabowlesphd.wordpress.com/
Email: bowlese at gmail.com
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