我正在使用Vegan和 ggplot来创建一个RDA图，但在处理点标签的混乱时遇到了困难。它们不易读，我尝试过只用少数字母的缩写，但并没有改善图形。是否可以从图中移除一些（重叠的）标签，调整间距以减少重叠？任何建议都会不胜感激！谢谢！

spe.rda.signif <- rda(phyla_hel ~ PFNA, data = pfas_sc)

## extract scores - these are coordinates in the RDA space
sc_si <- scores(spe.rda.signif, display="sites", choices=c(1,2), scaling=2)
sc_sp <- scores(spe.rda.signif, display="species", choices=c(1,2), scaling=2)
sc_bp <- scores(spe.rda.signif, display="bp", choices=c(1, 2), scaling=2)

plot(spe.rda.signif,
     scaling = 2, # 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)
     xlab = paste0("RDA1 (", perc[1], "%)"), 
     ylab = paste0("RDA2 (", perc[2], "%)") 
)
# add points for site scores
points(sc_si, 
       pch = 21, # set shape (here, circle with a fill colour)
       col = "black", # outline colour
       bg = "steelblue", # fill colour
       cex = 1.2) # size
# add points for species scores
points(sc_sp, 
       pch = 22, # set shape (here, square with a fill colour)
       col = "black",
       bg = "#f2bd33", 
       cex = 1.2)
# add text labels for species abbreviations
text(sc_sp + c(0.03, 0.09), # adjust text coordinates to avoid overlap with points 
     labels = rownames(sc_sp), 
     col = "grey40", 
     font = 2, # bold
     cex = 0.8)
# add arrows for effects of the expanatory variables
arrows(0,0, # start them from (0,0)
       sc_bp[,1], sc_bp[,2], # end them at the score value
       col = "red", 
       lwd = 3)

# add text labels for arrows
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 = 2)

解决方案

在RDA图中避免混乱可能做不到。不过，在适度混乱的情况下，以下方法在当前vegan版本中可能奏效（CRAN现有版本为2.7-3）：

plot(spe.rda.signif, spe.par = list(optimize=TRUE, type="t"),
     sit.par = list(type="p"))

或者你也可以使用管道（在当前vegan版本中也可用）：

plot(spe.rda.signif, type = "n") |>
   points("sites", cex=0.7) |>
   text("species", col="red", cex=0.7, optimize=TRUE) |>
   text("biplot", col="blue")

如果你想使用ggplot2，我建议尝试ggvegan：

library(ggvegan) # ordiggplot, ggscores, geom_ordi_*
library(ggplot2)
library(ggrepel) # geom_*_repel
ordiggplot(spe.rda.signif) +
   geom_ordi_axis() +
   geom_ordi_point("sites") +
   geom_ordi_point("species", col="red") +
   geom_text_repel(data=ggscores("species"), col="red") +
   geom_ordi_arrow("biplot", col="blue")