[adegenet-forum] labeling individuals in scatter pot

[pablo fresia]

... 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
>
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