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.