RDA triplot in R- plot only numeric explanatory variables as arrows; factors as centroids

Question

I ran a distance-based RDA using capscale() in the vegan library in R and I am trying to plot my results as a custom triplot. I only want numeric or continuous explanatory variables to be plotted as arrows/vectors. Currently, both factors and numeric explanatory variables are being plotted with arrows, and I want to remove arrows for factors (site and year) and plot centroids for these instead.

dbRDA=capscale(species ~ canopy+gmpatch+site+year+Condition(pair), data=env, dist="bray")

To plot I extracted % explained by the first 2 axes as well as scores (coordinates in RDA space)

perc <- round(100*(summary(spe.rda.signif)$cont$importance[2, 1:2]), 2)
sc_si <- scores(spe.rda.signif, display="sites", choices=c(1,2), scaling=1)
sc_sp <- scores(spe.rda.signif, display="species", choices=c(1,2), scaling=1)
sc_bp <- scores(spe.rda.signif, display="bp", choices=c(1, 2), scaling=1)

I then set up a blank plot with scaling, axes, and labels

dbRDAplot<-plot(spe.rda.signif,
     scaling = 1, # set scaling type 
     type = "none", # this excludes the plotting of any points from the results
     frame = FALSE,
     # set axis limits
     xlim = c(-1,1), 
     ylim = c(-1,1),
     # label the plot (title, and axes)
     main = "Triplot db-RDA - scaling 1",
     xlab = paste0("db-RDA1 (", perc[1], "%)"), 
     ylab = paste0("db-RDA2 (", perc[2], "%)"))

Created a legend and added points for site scores and text for species

pchh <- c(2, 17, 1, 19)
ccols <- c("black", "red", "black", "red")
legend("topleft", c("2016 MC", "2016 SP", "2018 MC", "2018 SP"), pch = pchh[unique(as.numeric(as.factor(env$siteyr)))], pt.bg = ccols[unique(as.factor(env$siteyr))], bty = "n")

points(sc_si, 
       pch = pchh[as.numeric(as.factor(env$siteyr))], # set shape 
       col = ccols[as.factor(env$siteyr)], # outline colour
       bg = ccols[as.factor(env$siteyr)], # fill colour
       cex = 1.2) # size

text(sc_sp , # text(sc_sp + c(0.02, 0.08) tp adjust text coordinates to avoid overlap with points 
     labels = rownames(sc_sp), 
     col = "black", 
     font = 1, # bold
     cex = 0.7)

Here is where I add arrows for explanatory variables, but I want to be selective and do so for numeric variables only (canopy and gmpatch). The variables site and year I want to plot as centroids, but unsure how to do this. Note that the data structure for these are definitely specified as factors already.

arrows(0,0, # start them from (0,0)
       sc_bp[,1], sc_bp[,2], # end them at the score value
       col = "red", 
       lwd = 2)

text(x = sc_bp[,1] -0.1, # adjust text coordinate to avoid overlap with arrow tip
     y = sc_bp[,2] - 0.03, 
     labels = rownames(sc_bp), 
     col = "red", 
     cex = 1, 
     font = 1)

@JariOksanen thank you for your answer. I was able to use the following to fix the problem

text(dbRDA, choices = c(1, 2),"cn", arrow=FALSE, length=0.05, col="red", cex=0.8, xpd=TRUE) 

text(dbRDA, display = "bp", labels = c("canopy", "gmpatch"), choices = c(1, 2),scaling = "species", arrow=TRUE, select = c("canopy", "gmpatch"), col="red", cex=0.8, xpd = TRUE)

Answer 1

@JariOksanen thank you for your answer. I was able to use the following to fix the problem

text(dbRDA, choices = c(1, 2),"cn", arrow=FALSE, length=0.05, col="red", cex=0.8, xpd=TRUE) 

text(dbRDA, display = "bp", labels = c("canopy", "gmpatch"), choices = c(1, 2),scaling = "species", arrow=TRUE, select = c("canopy", "gmpatch"), col="red", cex=0.8, xpd = TRUE)