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$where]
Here's my version:
where = c (3, 3, 8, 6, 6, 9, 5, 5, 9, 3, 8, 6, 9, 6, 5, 9, 5, 3, 8, 6,
9, 6, 5, 9, 5, 3, 3, 8, 6, 6, 9, 5, 5, 9, 6, 9, 5, 9)
unique (where)
c("red", "green", "blue", "aquamarine", "magenta")[where]
There's five colors.
But only two of the indices are within one to five.
So, the resulting color vector contains missing values.
In the base graphics system, if you set colors to NA, it usually means no color.
I'm not sure exactly what you want to do, but I'm assuming you can fix
it from here.
On Tue, Aug 4, 2020 at 9:49 PM Andrew Halford wrote:
>
> Hi,
>
> I've been trying to use the output on group membership of the final leaves
> in a MRT analysis to define my own colours, however I am not getting the
> result I'm after.
>
> Here is the code
> fish.pca <-rda(fish_all.hel,scale=TRUE)
> fish.site <- scores(fish.pca,display="sites",scaling=3)
> fish.spp <-
> scores(fish.pca,display="species",scaling=3)[fish.MRT.indval$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]]
>
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