[adegenet-forum] Dots in the DAPC graphic (Lucas Veiga)
Shannon O'Leary
shannon.j.oleary at gmail.com
Mon Oct 16 21:29:04 CEST 2017
Hi Lucas,
Try this on for size:
>From your description it looks like you have a data set for which you have
the following information:
SAMPLE-ID | POPULATION (CROP) | GENOTYPES
you read in the genotypes as a genind object (gen) and your can read in
your sample information as a dataframe containing Sample_ID and POP
information (SampleInfo)
You then ran k-means clustering/DAPC on your data set, something like this
grp <- find.clusters.genind(gen, n.pca = 200,
stat = "BIC", choose.n.clust = FALSE, criterion
= "min",
max.n.clust = 40)
dapc <-dapc(gen, grp$grp, n.pca = 50, n.da = 2)
You can pull the information on which sample was assigned to which cluster
like so:
clusters <- as.data.frame(grp$grp) %>%
rownames_to_column("SAMPLE_ID") %>%
rename(CLUSTER = `grp$grp`)
You can add this information to your SampleInfo dataframe using
dplyr::left_join()
SampleInfo <- left_join(SampleInfo, clusters, by = "SAMPLE_ID")
resulting in a dataframe with 3 columns: SAMPLE_ID | CROP | CLUSTER.
Now you can pull the coordinates from the dapc and also add them to that
data frame as well:
DAPC_Ind <- as.data.frame(dapc$ind.coord) %>%
rownames_to_column("SAMPLE_ID")
SampleInfo <- left_join(SampleInfo, DAPC_Ind, by = "SAMPLE_ID")
Now you have a data frame that should look something like this
SAMPLE_ID | CROP | CLUSTER | LD1 | LD2 ...
Now you can plot your data using ggplot and you can adjust the shape and
color of your data points as you please, for example:
ggplot(SampleInfo, aes(x = LD1, y = LD2), color = CROP, shape = CLUSTER) +
geom_point()
Is this what you are trying to achieve? You'll have to tweak the "code"
I've thrown in here to fit your data (column names etc).
Shannon
><(((jº> ><(((jº> ><(((jº> ><(((jº> ><(((jº> ><(((jº> ><(((jº>
Shannon J. O'Leary
Postdoctoral Research Associate
Marine Genomics Lab
Life Science Department
Texas A&M Corpus Christi
On Mon, Oct 16, 2017 at 12:11 PM, <
adegenet-forum-request at lists.r-forge.r-project.org> wrote:
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> 1. Re: Dots in the DAPC graphic (Lucas Veiga)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 16 Oct 2017 17:10:49 +0000 (UTC)
> From: Lucas Veiga <lucasfip at yahoo.com.br>
> To: Zhian Kamvar <zkamvar at gmail.com>,
> "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: <1729769391.894921.1508173849615 at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear All (Kamvar, Jombart and Roman),First, I would like to thank you all
> for spending a little of your time on my problem. Unfortunely, it was not
> possible to do what I want with commands that you showed me. I think that I
> will have to write very? carefully my work to explain my groups and my dots
> (haployd individuals) inside of the groups formed by DAPC analysis.?Obs:
> Kamvar, your command is very useful, but it was not possible to have dots
> with different colors or forms inside of the same group.
>
> Best regards,Lucas Veiga Ayres Pimenta
>
> Em Sexta-feira, 13 de Outubro de 2017 12:48, Zhian Kamvar <
> zkamvar at gmail.com> escreveu:
>
>
> 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, the results of which look like
> so:?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 PathologyUniversity of Nebraska-LincolnORCID:?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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> Today's Topics:
>
> ??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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