[R] Fwd: defining group colours in a call to rda

[Andrew Halford]

---------- Forwarded message ---------
From: Abby Spurdle <spurdle.a using gmail.com>
Date: Wed, Aug 5, 2020 at 3:07 PM
Subject: Re: [R] defining group colours in a call to rda
To: Andrew Halford <andrew.halford using gmail.com>


Hi Andrew,

Perhaps you want this:

    cols <- rep_len (c ("red", "green", "blue", "aquamarine", "magenta"), 9)
    cols

Or this:

    cols = rep ("", 9)
    cols [unique (MI_fish_all.mrt$where)] = c ("red", "green", "blue",
"aquamarine", "magenta")
    cols

Then you can substitute either into your original example:

    plotcolor <- cols [MI_fish_all.mrt$where]


On Wed, Aug 5, 2020 at 1:02 PM Andrew Halford <andrew.halford using gmail.com>
wrote:
>
> Hi Abby,
>
> Apologies for not providing more info but you have worked out what I was
on about anyways.
>
> I thought it would scroll through and allocate the colours to each unique
number sequentially. I will add more colours to my vector but I would like
to know if it is possible to do what I originally hoped for.
>
> cheers
>
> Andy
>
> On Wed, Aug 5, 2020 at 8:40 AM Abby Spurdle <spurdle.a using gmail.com> wrote:
>>
>> Hi,
>>
>> Your example is not reproducible.
>> However, I suspect that the following is the problem:
>>
>> c("red","green","blue","aquamarine","magenta")[MI_fish_all.mrt$where]
>>
>> Here's my version:
>>
>> where = c (3, 3, 8, 6, 6, 9, 5, 5, 9, 3, 8, 6, 9, 6, 5, 9, 5, 3, 8, 6,
>> 9, 6, 5, 9, 5, 3, 3, 8, 6, 6, 9, 5, 5, 9, 6, 9, 5, 9)
>> unique (where)
>>
>> c("red", "green", "blue", "aquamarine", "magenta")[where]
>>
>> There's five colors.
>> But only two of the indices are within one to five.
>> So, the resulting color vector contains missing values.
>>
>> In the base graphics system, if you set colors to NA, it usually means
no color.
>>
>> I'm not sure exactly what you want to do, but I'm assuming you can fix
>> it from here.
>>
>> On Tue, Aug 4, 2020 at 9:49 PM Andrew Halford <andrew.halford using gmail.com>
wrote:
>> >
>> > Hi,
>> >
>> > I've been trying to use the output on group membership of the final
leaves
>> > in a MRT analysis to define my own colours, however I am not getting
the
>> > result I'm after.
>> >
>> > Here is the code
>> > fish.pca <-rda(fish_all.hel,scale=TRUE)
>> > fish.site <- scores(fish.pca,display="sites",scaling=3)
>> > fish.spp <-
>> >
scores(fish.pca,display="species",scaling=3)[fish.MRT.indval$pval<=0.05,]
>> > plot(fish.pca,display=c("sites","species"),type="n",scaling=3)
>> > points(fish.site,pch=21,bg=MI_fish_all.mrt$where,cex=1.2)
>> > plotcolor <-
>> > c("red","green","blue","aquamarine","magenta")[MI_fish_all.mrt$where]
>> >  fish.pca <-rda(fish_all.hel,scale=TRUE)
>> > plot(fish.pca,display=c("sites","species"),type="n",scaling=3)
>> > points(fish.site,pch=21,bg=plotcolor,cex=1.2)
>> > MI_fish_all.mrt$where
>> >
>> > If I run the points command and insert the group membership direct
from the
>> > MRT analysis e.g.  bg=MI_fish_all.mrt$where , then the subsequent
points
>> > plot up correctly with a different colour for each group.However if I
try
>> > to impose my own colour combo with plotcolor.....It prints colours for
2
>> > groups and leaves the rest uncoloured.
>> >
>> > The call to  MI_fish_all.mrt$where gives...
>> >  [1] 3 3 8 6 6 9 5 5 9 3 8 6 9 6 5 9 5 3 8 6 9 6 5 9 5 3 3 8 6 6 9 5 5
9 6
>> > 9 5 9.
>> >
>> > These are the split groupings for all 39 sites in the analysis and
there
>> > are 5 numbers corresponding to 5 final leaves in the tree.
>> >
>> > I cant see why my colour scheme isnt being recognised.
>> >
>> > All help accepted.
>> >
>> > Andy
>> >
>> >
>> > --
>> > Andrew Halford Ph.D
>> > Senior Coastal Fisheries Scientist
>> > Pacific Community | Communauté du Pacifique CPS – B.P. D5 | 98848
Noumea,
>> > New Caledonia | Nouméa, Nouvelle-Calédonie
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
> --
> Andrew Halford Ph.D
> Senior Coastal Fisheries Scientist
> Pacific Community | Communauté du Pacifique CPS – B.P. D5 | 98848 Noumea,
> New Caledonia | Nouméa, Nouvelle-Calédonie


-- 
Andrew Halford Ph.D
Senior Coastal Fisheries Scientist
Pacific Community | Communauté du Pacifique CPS – B.P. D5 | 98848 Noumea,
New Caledonia | Nouméa, Nouvelle-Calédonie

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