I am plotting biplots of NMDS and using ggforce::geom_marK_hull to create hulls around points representing fish communities from two sites, faceted by year and season (wet and dry): Biplot
I found that some of the hulls are including empty spaces without any points (e.g. Upstream group in wet season 2018 and Upstream group in dry season 2020). I have tried to adjust the expand argument but it seems the problem persists.
Any idea what the reason might be? I would appreciate any comments or help! Thanks in advance!
Raw data files used are fish.spp and fish.env. Codes are:
library(vegan)
library(ggplot2)
library(ggforce)
library(concaveman)
fish.nmds.k3 <- metaMDS(fish.spp, distance = "bray", k = 3)
fish.nmds.k3.sites <- as.data.frame(fish.nmds.k3$points)
fish.nmds.k3.sp <- as.data.frame(fish.nmds.k3$species)
(ggplot(fish.nmds.k3.sites, aes(MDS1, MDS2))+
ylim(-3, 3) + xlim (-3, 3) +
geom_mark_hull(aes(fill = fish.env$Site), expand = unit(3, "mm")) +
geom_point() +
labs(title = "NMDS Plot of Freshwater Fish Community") +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5, face = "bold", size = 10),
panel.grid = element_blank()) +
facet_grid(rows = vars(fish.env$Year), cols = vars(fish.env$Season))
)