[adegenet-forum] Dots in the DAPC graphic
Zhian Kamvar
zkamvar at gmail.com
Fri Oct 13 17:47:54 CEST 2017
Hi,
The individual coordinates are in the @ind.coord slot of the DAPC object. You can use those to plot and color them with your desired population factor.
I have recently come up with a ggplot2 solution for this: https://github.com/everhartlab/sclerotinia-366/blame/v1.0/results/by-year.md#L508-L558 <https://github.com/everhartlab/sclerotinia-366/blame/v1.0/results/by-year.md#L508-L558>, the results of which look like so: https://github.com/everhartlab/sclerotinia-366/blob/v1.0/results/figures/by-year/dapc_plot-2.png <https://github.com/everhartlab/sclerotinia-366/blob/v1.0/results/figures/by-year/dapc_plot-2.png>
Hope that helps,
Zhian
-----
Zhian N. Kamvar, Ph. D.
Postdoctoral Researcher (Everhart Lab)
Department of Plant Pathology
University of Nebraska-Lincoln
ORCID: 0000-0003-1458-7108
> On Oct 13, 2017, at 03:39 , adegenet-forum-request at lists.r-forge.r-project.org wrote:
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> 1. Re: Dots in the DAPC graphic (Lucas Veiga)
> 2. Re: Dots in the DAPC graphic (Lucas Veiga)
> 3. Re: Dots in the DAPC graphic (Roman Lu?trik)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 12 Oct 2017 12:03:35 +0000 (UTC)
> From: Lucas Veiga <lucasfip at yahoo.com.br>
> To: Roman Lu?trik <roman.lustrik at biolitika.si>
> Cc: "adegenet-forum at lists.r-forge.r-project.org"
> <adegenet-forum at lists.r-forge.r-project.org>
> Subject: Re: [adegenet-forum] Dots in the DAPC graphic
> Message-ID: <1994389766.433362.1507809815326 at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Roman,First, thank you for the help. Unfortunaly, apparently your command not worked for me. I will try explain better my situation. I work with phytopathology and the fungus that I work affects different crops (I have put in my input file .csv the crops as my populations, different crops are different populations). Due the migration of genotypes of the fungus between the crops, inside of one group formed by DAPC there are genotypes obtained of different crops (populations) and for better viewing of this migration I want to plot the dots according of the hosts and not according of the groups formed by DAPC analysis. So, inside of one group there will are dots of different colors.?I hope have explain better my situation and that you can help me.
> Best regards,Lucas Veiga Ayres pimenta
>
> Em Quinta-feira, 12 de Outubro de 2017 5:49, Roman Lu?trik <roman.lustrik at biolitika.si> escreveu:
>
>
> Map `grp` argument to your desired grouping. Make sure that you pass `col` the correct number of colors which should match the number of groups you are specifying.
> By default, coloring is done on grouping (see here). See this example:
> library(adegenet)
>
> data(H3N2)
> pop(H3N2) <- factor(H3N2$other$epid)
> dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)
>
> data.frame(dapc1$grp, pop(H3N2)) # they are matching
>
> Cheers,Roman
>
>
> ----
> In god we trust, all others bring data.
>> Zahtevaj IJZ na https://kurc.biolitika.si
> From: "Lucas Veiga" <lucasfip at yahoo.com.br>
> To: adegenet-forum at lists.r-forge.r-project.org
> Sent: Thursday, October 12, 2017 1:34:19 AM
> Subject: [adegenet-forum] Dots in the DAPC graphic
>
> Dear all,I would like to know what I can do for the dots in DAPC graph to be colored according to the populations and not according to the DAPC analysis groups?
>
> Best regards,
> Lucas Veiga Ayres Pimenta
> _______________________________________________
> 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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> ------------------------------
>
> Message: 2
> Date: Thu, 12 Oct 2017 12:10:28 +0000 (UTC)
> From: Lucas Veiga <lucasfip at yahoo.com.br>
> To: Roman Lu?trik <roman.lustrik at biolitika.si>
> Cc: "adegenet-forum at lists.r-forge.r-project.org"
> <adegenet-forum at lists.r-forge.r-project.org>
> Subject: Re: [adegenet-forum] Dots in the DAPC graphic
> Message-ID: <342879047.415645.1507810228644 at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Roman,First, thank you for the help. Unfortunaly, apparently your command not worked for me. I will try explain better my situation. I work with phytopathology and the fungus that I work affects different crops (I have put in my input file .csv the crops as my populations, different crops are different populations). Due the migration of genotypes of the fungus between the crops, inside of one group formed by DAPC there are genotypes obtained of different crops (populations) and for better viewing of this migration I want to plot the dots according to the hosts and not according to the groups formed by DAPC analysis. So, inside of one group there will are dots of different colors.?I hope I have explained better my situation and that you can help me.
> Best regards,Lucas Veiga Ayres pimenta
>
> Em Quinta-feira, 12 de Outubro de 2017 9:03, Lucas Veiga <lucasfip at yahoo.com.br> escreveu:
>
>
> Dear Roman,First, thank you for the help. Unfortunaly, apparently your command not worked for me. I will try explain better my situation. I work with phytopathology and the fungus that I work affects different crops (I have put in my input file .csv the crops as my populations, different crops are different populations). Due the migration of genotypes of the fungus between the crops, inside of one group formed by DAPC there are genotypes obtained of different crops (populations) and for better viewing of this migration I want to plot the dots according of the hosts and not according of the groups formed by DAPC analysis. So, inside of one group there will are dots of different colors.?I hope have explain better my situation and that you can help me.
> Best regards,Lucas Veiga Ayres pimenta
>
> Em Quinta-feira, 12 de Outubro de 2017 5:49, Roman Lu?trik <roman.lustrik at biolitika.si> escreveu:
>
>
> Map `grp` argument to your desired grouping. Make sure that you pass `col` the correct number of colors which should match the number of groups you are specifying.
> By default, coloring is done on grouping (see here). See this example:
> library(adegenet)
>
> data(H3N2)
> pop(H3N2) <- factor(H3N2$other$epid)
> dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)
>
> data.frame(dapc1$grp, pop(H3N2)) # they are matching
>
> Cheers,Roman
>
>
> ----
> In god we trust, all others bring data.
>> Zahtevaj IJZ na https://kurc.biolitika.si
> From: "Lucas Veiga" <lucasfip at yahoo.com.br>
> To: adegenet-forum at lists.r-forge.r-project.org
> Sent: Thursday, October 12, 2017 1:34:19 AM
> Subject: [adegenet-forum] Dots in the DAPC graphic
>
> Dear all,I would like to know what I can do for the dots in DAPC graph to be colored according to the populations and not according to the DAPC analysis groups?
>
> Best regards,
> Lucas Veiga Ayres Pimenta
> _______________________________________________
> 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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> ------------------------------
>
> Message: 3
> Date: Fri, 13 Oct 2017 10:38:57 +0200 (CEST)
> From: Roman Lu?trik <roman.lustrik at biolitika.si>
> To: Lucas Veiga <lucasfip at yahoo.com.br>
> Cc: adegenet-forum at lists.r-forge.r-project.org
> Subject: Re: [adegenet-forum] Dots in the DAPC graphic
> Message-ID:
> <181441774.286421.1507883937636.JavaMail.zimbra at biolitika.si>
> Content-Type: text/plain; charset="utf-8"
>
> A-ha, I think I see where you're getting at. Right now I'm not sure it's possible to have DAPC groups with samples colored by some specific variable. Perhaps Thibaut will be able to chime in. If I'm right, this is something we could think about in the upcoming releases.
>
> In the mean time, you can construct your own plot, taking bits and pieces from https://github.com/thibautjombart/adegenet/blob/master/R/dapc.R#L539
>
>
>
> Cheers,
> Roman
>
> ----
> In god we trust, all others bring data.
>> Zahtevaj IJZ na https://kurc.biolitika.si
>
>
> From: "Lucas Veiga" <lucasfip at yahoo.com.br>
> To: "Roman Lu?trik" <roman.lustrik at biolitika.si>
> Cc: adegenet-forum at lists.r-forge.r-project.org
> Sent: Thursday, October 12, 2017 2:03:35 PM
> Subject: Re: [adegenet-forum] Dots in the DAPC graphic
>
> Dear Roman,
> First, thank you for the help. Unfortunaly, apparently your command not worked for me. I will try explain better my situation. I work with phytopathology and the fungus that I work affects different crops (I have put in my input file .csv the crops as my populations, different crops are different populations). Due the migration of genotypes of the fungus between the crops, inside of one group formed by DAPC there are genotypes obtained of different crops (populations) and for better viewing of this migration I want to plot the dots according of the hosts and not according of the groups formed by DAPC analysis. So, inside of one group there will are dots of different colors.
> I hope have explain better my situation and that you can help me.
>
> Best regards,
> Lucas Veiga Ayres pimenta
>
>
> Em Quinta-feira, 12 de Outubro de 2017 5:49, Roman Lu?trik <roman.lustrik at biolitika.si> escreveu:
>
>
> Map `grp` argument to your desired grouping. Make sure that you pass `col` the correct number of colors which should match the number of groups you are specifying.
> By default, coloring is done on grouping ( see here ). See this example:
>
> library(adegenet)
>
> data(H3N2)
> pop(H3N2) <- factor(H3N2$other$epid)
> dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)
>
> data.frame(dapc1$grp, pop(H3N2)) # they are matching
>
> Cheers,
> Roman
>
>
>
> ----
> In god we trust, all others bring data.
>> Zahtevaj IJZ na https://kurc.biolitika.si
>
>
> From: "Lucas Veiga" <lucasfip at yahoo.com.br>
> To: adegenet-forum at lists.r-forge.r-project.org
> Sent: Thursday, October 12, 2017 1:34:19 AM
> Subject: [adegenet-forum] Dots in the DAPC graphic
>
> Dear all,
> I would like to know what I can do for the dots in DAPC graph to be colored according to the populations and not according to the DAPC analysis groups?
>
> Best regards,
> Lucas Veiga Ayres Pimenta
>
> _______________________________________________
> 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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