From kimash21 at gmail.com  Mon Jul 16 00:20:31 2018
From: kimash21 at gmail.com (Kimani Kitson-Walters)
Date: Sun, 15 Jul 2018 18:20:31 -0400
Subject: [adegenet-forum] Insert Legend when mapping PC of DAPC using
	colorplot()
Message-ID: <CAP38GpHNxHuQU1+OycK-wJFM-o9jK7esnTwEYxpmO7H8BM=1gA@mail.gmail.com>

Hello Fellow adegenet users,

I need your help :)

I have run a DAPC on individuals from 5 sites and have mapped the results
using the colorplot() function. The resulting map shows the average DAPC
score for each site by converting the score for each site into a colour
with sites with similar colours being more related and vice versa.

How do I insert a legend to indicate what the relationship of the colours
mean? I assume you can use the legend() function but how do I give it the
average DAPC scores so it can translate it into a colour scale?

I hope someone can help me. I would really appreciate it.

Kimani Kitson-Walters
Data Monitoring Officer
Caribbean Netherlands Science Institue
St. Eustatius
-- 


Mr. Kimani Kitson-Walters BSc (Hons)
PhD Candidate
University of the West Indies, Mona
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From thibautjombart at gmail.com  Mon Jul 16 12:08:18 2018
From: thibautjombart at gmail.com (Thibaut Jombart)
Date: Mon, 16 Jul 2018 11:08:18 +0100
Subject: [adegenet-forum] Insert Legend when mapping PC of DAPC using
	colorplot()
In-Reply-To: <CAP38GpHNxHuQU1+OycK-wJFM-o9jK7esnTwEYxpmO7H8BM=1gA@mail.gmail.com>
References: <CAP38GpHNxHuQU1+OycK-wJFM-o9jK7esnTwEYxpmO7H8BM=1gA@mail.gmail.com>
Message-ID: <CANPRA+qrDfHS6zyPseJmdPRC-8dYCkYDkmu9De6c5J0RC-uA5g@mail.gmail.com>

Hi Kimani,

this is a good question, but I'm afraid there's no good answer to it. How
many dimensions did you map into colors? If more than one, say 2, then
providing a legend is quite hard, as your legend itself should be
2-dimensional (run example(colorplot) for an example of 2d color map). For
3 dimensions, that's even worse.

In short: for a one-dimensional color, that's pretty easy, and not really
feasible beyond. For publication purposes, you could present the colorplot
as a synthesis figure, and use individual maps for separate axes.

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
WHO Consultant - outbreak analysis
https://thibautjombart.netlify.com
Twitter: @TeebzR
+44(0)20 7594 3658

On 15 July 2018 at 23:20, Kimani Kitson-Walters <kimash21 at gmail.com> wrote:

> Hello Fellow adegenet users,
>
> I need your help :)
>
> I have run a DAPC on individuals from 5 sites and have mapped the results
> using the colorplot() function. The resulting map shows the average DAPC
> score for each site by converting the score for each site into a colour
> with sites with similar colours being more related and vice versa.
>
> How do I insert a legend to indicate what the relationship of the colours
> mean? I assume you can use the legend() function but how do I give it the
> average DAPC scores so it can translate it into a colour scale?
>
> I hope someone can help me. I would really appreciate it.
>
> Kimani Kitson-Walters
> Data Monitoring Officer
> Caribbean Netherlands Science Institue
> St. Eustatius
> --
>
>
> Mr. Kimani Kitson-Walters BSc (Hons)
> PhD Candidate
> University of the West Indies, Mona
>
> _______________________________________________
> 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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