[adegenet-forum] labeling individuals in scatter pot

[Nicolas Dussex]

Hi Pablo,

well, I tried but it does pretty much the same thing (i.e. 1 color per pop
and no info on the moprhology, for the latter a file with morphology info
is needed). Also I get this error message:

> myCol <- c("darkblue","darkgreen","red")
> scatter(dapc1, scree.da=FALSE, bg="white", pch=20, solid=.4, cex=0,
cstar=1, clab=1, col=myCol)
> par(xpd=TRUE)
> points(dapc$ind.coord[1:90,],
+        pch=17, cex=1, col="black")
*Error in dapc$ind.coord : object of type 'closure' is not subsettable*
> par(xpd=TRUE)
> points(dapc$ind.coord[91:218,],
+        pch=18, cex=1.4, col="black")
*Error in dapc$ind.coord : object of type 'closure' is not subsettable*
> par(xpd=TRUE)
> points(dapc$ind.coord[219:326,],
+        pch=21, cex=1, col="black")
*Error in dapc$ind.coord : object of type 'closure' is not subsettable*
> par(xpd=TRUE)
> points(dapc$ind.coord[327:392,],
+        pch=20, cex=1.3, col="black")
*Error in dapc$ind.coord : object of type 'closure' is not subsettable*

Cheers
Nic

On 30 April 2015 at 13:03, pablo fresia <pfresia at gmail.com> wrote:

> Hi Nicolas,
>
> what's going on, if you try something like this below ?
>
> myCol <- c("darkblue","darkgreen","red")
> scatter(dapc, scree.da=FALSE, bg="white", pch=20, solid=.4, cex=0,
> cstar=1, clab=1, col=myCol)
> par(xpd=TRUE)
> points(dapc$ind.coord[1:90,],
>        pch=17, cex=1, col="black")
> par(xpd=TRUE)
> points(dapc$ind.coord[91:218,],
>        pch=18, cex=1.4, col="black")
> par(xpd=TRUE)
> points(dapc$ind.coord[219:326,],
>        pch=21, cex=1, col="black")
> par(xpd=TRUE)
> points(dapc$ind.coord[327:392,],
>        pch=20, cex=1.3, col="black")
>
> good luck!
> pablo
>
>
> On 29 April 2015 at 21:50, Nicolas Dussex <nicolas.dussex at gmail.com>
> wrote:
>
>> Hi,
>>
>> I am doing a DAPC for a dataset that contains 6 populations. Among all my
>> samples, there are three different morphs and each population contains a
>> variable mixture of each. What I want to do is to use a different color for
>> each population (I managed to do it) and use a different type of point for
>> each sample according to its moprhotype. I have a file that contains this
>> info ( 1 colomn with either X, W or WR).
>>
>> I tried using pch as described below, but the labels do not correspond to
>> the individuals.
>>
>> dapc1 <- dapc(Z1, n.pca = 10, n.da = 3)
>> c<-morph_data_6m[,1]
>> scatter(dapc1, cstar=0,cex=2.5, cell=0, label=NULL, leg =
>> TRUE,scree.da=FALSE,txt.leg =
>> c("233","287","418","674","878","957","1085"), *pch=c*)
>>
>> Would there be a way to assign to each individual a type of point
>> corresponding to its morphotype? Say point for W, star for X and triangle
>> for WR.
>>
>> Thanks for your help!
>> Nic
>>
>>
>> --
>> Nic Dussex PhD
>> Department of Zoology
>> University of Otago
>> 340 Great King Street
>> P.O.Box 56
>> Dunedin 9054
>> New Zealand
>>
>> Mobile: +64 21 02790938
>>
>> _______________________________________________
>> 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
>>
>
>


-- 
Nic Dussex PhD
Department of Zoology
University of Otago
340 Great King Street
P.O.Box 56
Dunedin 9054
New Zealand

Mobile: +64 21 02790938
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20150430/e02c963c/attachment.html>