I created an object of class cca in vegan and now I am trying to tidy up the triplot. However, I seemingly can't use the select argument to only show specified items. My code looks like this:
data("varechem")
data("varespec")
ord <- cca(varespec ~ Al+S, varechem)
plot(ord, type = "n")
text(ord, display = "sites", select = c("18", "21"))
I want only the two specified sites (18 and 21) to appear in the plot, but when I run the code nothing happens. I do not even get an error meassage.
I'm really stuck, but I am fairly certain that this bit of code is correct. Can someone help me?
I can't recall now, but I don't think the intention was to allow "names" to select which rows of the scores should be selected. The documentation speaks of select being a logical vector, or indices of the scores to be selected. By indices it was meant numeric indices, not rownames.
The example fails because select is also used to subset the labels character vector of values to be plotted in text(), and this labels character vector is not named. Using a character vector to subset another vector requires that the other vector be named.
Your example works if you do:
data("varechem")
data("varespec")
ord <- cca(varespec ~ Al + S, varechem)
plot(ord, type = "n")
take <- which(rownames(varechem) %in% c("18", "21"))
# or
# take <- rownames(varechem) %in% c("18", "21")
text(ord, display = "sites", select = take)
I'll have a think about whether it will be simple to support the use case of your example.