[adegenet-forum] Dots in the DAPC graphic

[Roman Luštrik]

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 Luštrik" <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 Luštrik <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 

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