Customising vegan ordination plot - r

Question

I have a dataset including 100 species and therefore it's very bad to plot. So I want to pick out a subset of these species and plot them in a RDA plot. I have been following this
guideline
The code looks like this:
## load vegan
require("vegan")
## load the Dune data
data(dune, dune.env)
## PCA of the Dune data
mod <- rda(dune, scale = TRUE)
## plot the PCA
plot(mod, scaling = 3)
## build the plot up via vegan methods
scl <- 3 ## scaling == 3
colvec <- c("red2", "green4", "mediumblue")
plot(mod, type = "n", scaling = scl)
with(dune.env, points(mod, display = "sites", col = colvec[Use],
scaling = scl, pch = 21, bg = colvec[Use]))
text(mod, display = "species", scaling = scl, cex = 0.8, col = "darkcyan")
with(dune.env, legend("topright", legend = levels(Use), bty = "n",
col = colvec, pch = 21, pt.bg = colvec))
This is the plot you end up with. Now i would really like to remove some of the species from the plot, but not the analysis. So the plot only shows like Salrep, Viclat, Aloge and Poatri.
Help is appreciated.

Answer 1

The functions you are doing the actual plotting with have an argument select (at least text.cca() and points.cca(). select takes either a logical vector of length i indicating whether the ith thing should be plotted, or the (numeric) indices of the things to plot. The example would then become:
## Load vegan
library("vegan")
## load the Dune data
data(dune, dune.env)
## PCA of the Dune data
mod <- rda(dune, scale = TRUE)
## plot the PCA
plot(mod, scaling = 3)
## build the plot up via vegan methods
scl <- 3 ## scaling == 3
colvec <- c("red2", "green4", "mediumblue")
## Show only these spp
sppwant <- c("Salirepe", "Vicilath", "Alopgeni", "Poatriv")
sel <- names(dune) %in% sppwant
## continue plotting
plot(mod, type = "n", scaling = scl)
with(dune.env, points(mod, display = "sites", col = colvec[Use],
scaling = scl, pch = 21, bg = colvec[Use]))
text(mod, display = "species", scaling = scl, cex = 0.8, col = "darkcyan",
select = sel)
with(dune.env, legend("topright", legend = levels(Use), bty = "n",
col = colvec, pch = 21, pt.bg = colvec))
Which gives you:

Answer 2

You may also use the ordiselect() function from the goeveg-package:
https://CRAN.R-project.org/package=goeveg
It offers selection of species for ordination plots based on abundances and/or species fit to axes.
## Select ssp. with filter: 50% most abundant and 50% best fitting
library(goeveg)
sel <- ordiselect(dune, mod, ablim = 0.5, fitlim = 0.5)
sel # 12 species selected
The result object of the function (containing the names of selected species) can be put into the select argument (as described above).