[adegenet-forum] labeling individuals in scatter pot

Nicolas Dussex nicolas.dussex at gmail.com
Fri May 1 00:48:13 CEST 2015 

humm.. I realise that it's gonna be difficult to do that with my 300+
samples so if someone has other suggestions, that would be fantastic.

Cheers
Nic

On 1 May 2015 at 10:05, Nicolas Dussex <nicolas.dussex at gmail.com> wrote:

> Thanks Pablo, seems to be working!
>
> Nic
>
> On 30 April 2015 at 14:28, pablo fresia <pfresia at gmail.com> wrote:
>
>> ... the errors are probably because of the bounds within [..., ...]
>>
>> I got this error message now:
>>>
>>> > points(dapc1$ind.coord[1:90,],
>>> +        pch=17, cex=1, col="black")
>>> Error in dapc1$ind.coord[1:90, ] : subscript out of bounds
>>> > par(xpd=TRUE)
>>> > points(dapc1$ind.coord[91:218,],
>>> +        pch=18, cex=1.4, col="black")
>>> Error in dapc1$ind.coord[91:218, ] : subscript out of bounds
>>> > par(xpd=TRUE)
>>> > points(dapc1$ind.coord[219:326,],
>>> +        pch=21, cex=1, col="black")
>>> Error in dapc1$ind.coord[219:326, ] : subscript out of bounds
>>> > par(xpd=TRUE)
>>> > points(dapc1$ind.coord[327:392,],
>>> +        pch=20, cex=1.3, col="black")
>>> Error in dapc1$ind.coord[327:392, ] : subscript out of bounds
>>>
>>> I thought about sorting indviduals by morphotype, but not sure how to do
>>> it as I want to keep the population info too. My samples are grouped by
>>> population at this stage.
>>>
>>
>> ... mixing both approaches may be you find a way. I figure, if you keep
>> the inds organized by pop but dividing it by morphotype you can assign
>> colors and symbols in the way you need.
>>
>> eg. pop 1: 1 to 30 inds, 1-15 morph 1 and 16-30 morph 2:
>>
>> > points(dapc1$ind.coord[1:15,], pch=17, cex=1, col="black")
>> > points(dapc1$ind.coord[16:30,], pch=18, cex=1, col="black")
>>
>> and so on...
>>
>> If I run this:
>>>
>>> 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)#col = myCol)
>>> par(new=TRUE)
>>> df <- data.frame(x = dapc1$ind.coord[,1], y = dapc1$ind.coord[,2])
>>> morph_data_6m<-read.table("morph_data_6m.txt", header=T)
>>> c<-morph_data_6m[,1]
>>> s.label(dfxy = df, xax=1, yax=2,
>>> label=c,clabel=0.7,boxes=FALSE,grid=FALSE, addaxes=FALSE)
>>>
>>> I obtain a plot of coloured dots corresponding to each population and I
>>> then add the morphotype label (W, WR or X; from my "moprh_data_6m.txt"
>>> file) on top of each dot, but it gets difficult to read when dots overlap
>>> (see example attached)
>>>
>>
>>  best
>> pablo
>>
>>
>>> On 30 April 2015 at 13:53, pablo fresia <pfresia at gmail.com> wrote:
>>>
>>>> ... maybe, the individuals needs to be by organized morphotype before
>>>> to run the DAPC.
>>>>
>>>> On 29 April 2015 at 22:49, pablo fresia <pfresia at gmail.com> wrote:
>>>>
>>>>> Hi Nic,
>>>>>
>>>>> an error, should be here
>>>>>
>>>>> > 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(*dapc1*$ind.coord[1:90,],
>>>>>> +        pch=17, cex=1, col="black")
>>>>>> *Error in dapc$ind.coord : object of type 'closure' is not
>>>>>> subsettable*
>>>>>> > par(xpd=TRUE)
>>>>>> > points(*dapc1*$ind.coord[91:218,],
>>>>>> +        pch=18, cex=1.4, col="black")
>>>>>> *Error in dapc$ind.coord : object of type 'closure' is not
>>>>>> subsettable*
>>>>>> > par(xpd=TRUE)
>>>>>> > points(*dapc1*$ind.coord[219:326,],
>>>>>> +        pch=21, cex=1, col="black")
>>>>>> *Error in dapc$ind.coord : object of type 'closure' is not
>>>>>> subsettable*
>>>>>> > par(xpd=TRUE)
>>>>>> > points(*dapc1*$ind.coord[327:392,],
>>>>>> +        pch=20, cex=1.3, col="black")
>>>>>> *Error in dapc$ind.coord : object of type 'closure' is not
>>>>>> subsettable*
>>>>>>
>>>>>
>>>>> cheers,
>>>>> pablo
>>>>>
>>>>>
>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> 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
>>>
>>
>>
>
>
> --
> 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
>



-- 
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
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