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