ordination

Code R de l'exemple ggplot2

library(ggplot2)
library(vegan)

## Principal coordinates of the Bray-Curtis dissimilarities between plots.
data(BCI, BCI.env)
pcoa <- cmdscale(vegdist(BCI, method = "bray"), k = 2, eig = TRUE)
share <- scales::percent(pcoa$eig[1:2] / sum(pcoa$eig[pcoa$eig > 0]), accuracy = 1)
habitats <- c(OldHigh = "Old, high plateau", OldLow = "Old, low plateau", OldSlope = "Old, slope",
              Swamp = "Swamp", Young = "Young forest")
plots <- data.frame(pcoa$points, habitat = habitats[as.character(BCI.env$Habitat)])

p <- ggplot(plots, aes(x = X1, y = X2, colour = habitat)) +
  geom_hline(yintercept = 0, colour = "#d6d6d6", linewidth = 0.3) +
  geom_vline(xintercept = 0, colour = "#d6d6d6", linewidth = 0.3) +
  geom_point(size = 2) +
  coord_fixed() +
  labs(title = "Slope and high-plateau plots separate along axis 1",
       subtitle = "PCoA of tree counts in 50 plots, Barro Colorado Island",
       x = paste0("Axis 1 (", share[1], ")"), y = paste0("Axis 2 (", share[2], ")"),
       colour = "Habitat",
       caption = "Data: Condit et al. 2002, via the vegan R package") +
  theme_lex_viz(grid = "", arrows = "") +
  theme(axis.text = element_blank(), legend.position = "right", legend.direction = "vertical")