You did not provide a reproducible example, but you should be able to get what
you want as follows:
library(vegan)
data(dune)
data(dune.env)
lbls <-as.integer(dune.env$Management)
grps <- levels(dune.env$Management)
ngrps <- length(grps)
example_dune <- metaMDS(dune, distance="bray", k=2)
ordiplot(example_dune, display="species", type="n")
points(example_dune, col="black", pch = lbls)
ordihull(example_dune, dune.env$Management, scaling = "symmetric",
lty=lbls)
# Optionally add a legend
legend("topright", grps, pch=1:ngrps, lty=1:ngrps)
# However if you want to position the labels, try this
grp.lbls <- locator()
# Click where you want each label to appear.
# The pch symbols are circle, triangle, plus, X
# click where you want the label to appear for each group
# in that order and then click stop (upper left corner)
# of the window.
text(grp.lbls, grps)
Or just eyeball the coordinates. Once you have them where you want them, save
them with dput() and include them in your script file (assuming you are planning
to plot to a print device later).
-------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352
-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Sibylle
St?ckli
Sent: Friday, December 9, 2016 12:20 PM
To: r-help at r-project.org
Subject: [R] vegan NMDS labels
Dear R users
Does anybody know how it may be possible to plot the labels of a ordihull
function separately (in R vegan)? We have studied the bee community in 5
different habitat types. As you see from the code, we use different point types
(pch) and line types (lty). This is only possible if we change the habitat from
character to integer. However, we prefer to show the labels as characters and
not as integers 1-5? Furthermore, does anybody now how to plot the labels at the
border and not in the centroid of the polygon (due to overlapping polygons it is
not easy to assign them to the right polygon)?
Many thanks
Sibylle
### NMDS code ####
example_NMDS=metaMDS(community_matrix, # Our community-by-species matrix
distance = "bray", k=2) # The number of reduced
dimensions
stressplot(example_NMDS)
ordiplot (example_NMDS, display = 'species', type = 'n',
xlim=c(-0.5,0.5), ylim=c(-0.7,0.7))
HabTyp<-as.integer(S1$H_Aggregat1) # 5 different habitats.
points (example_NMDS, col="black", pch = HabTyp)
for (i in unique (HabTyp)) ordihull (example_NMDS, groups = HabTyp, show.group =
i, draw = 'polygon', label=T, cex=1.5, lty=i)
[[alternative HTML version deleted]]
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