自定义素食排序图

Question

我有一个包含 100 个物种的数据集，因此很难绘制。所以我想挑选出这些物种的一个子集并将它们绘制在 RDA 图中。我一直在关注这个 guideline

代码如下所示：

## load vegan
require("vegan")

## load the Dune data
data(dune, dune.env)

## PCA of the Dune data
mod <- rda(dune, scale = TRUE)

## plot the PCA
plot(mod, scaling = 3)

## build the plot up via vegan methods
scl <- 3 ## scaling == 3
colvec <- c("red2", "green4", "mediumblue")
plot(mod, type = "n", scaling = scl)
with(dune.env, points(mod, display = "sites", col = colvec[Use],
                  scaling = scl, pch = 21, bg = colvec[Use]))
text(mod, display = "species", scaling = scl, cex = 0.8, col = "darkcyan")
with(dune.env, legend("topright", legend = levels(Use), bty = "n",
                  col = colvec, pch = 21, pt.bg = colvec))

这就是您最终得到的 plot。现在我真的很想从情节中删除一些物种，但不是分析。所以情节只显示像 Salrep、Viclat、Aloge 和 Poatri。

感谢您的帮助。

Answer 1

您在实际绘图时使用的函数有一个参数 select（至少 text.cca() 和 points.cca()。select 采用长度为 i 指示是否应绘制第 i 个事物，或要绘制的事物的（数字）索引。示例将变为：

## Load vegan
library("vegan")

## load the Dune data
data(dune, dune.env)

## PCA of the Dune data
mod <- rda(dune, scale = TRUE)

## plot the PCA
plot(mod, scaling = 3)

## build the plot up via vegan methods
scl <- 3 ## scaling == 3
colvec <- c("red2", "green4", "mediumblue")

## Show only these spp
sppwant <- c("Salirepe", "Vicilath", "Alopgeni", "Poatriv")
sel <- names(dune) %in% sppwant

## continue plotting
plot(mod, type = "n", scaling = scl)
with(dune.env, points(mod, display = "sites", col = colvec[Use],
                  scaling = scl, pch = 21, bg = colvec[Use]))
text(mod, display = "species", scaling = scl, cex = 0.8, col = "darkcyan",
     select = sel)
with(dune.env, legend("topright", legend = levels(Use), bty = "n",
                  col = colvec, pch = 21, pt.bg = colvec))

这给你：

Answer 2

您还可以使用 goeveg 包中的 ordiselect() 函数： https://CRAN.R-project.org/package=goeveg

它根据适合坐标轴的丰度 and/or 物种为排序图提供物种选择。

## Select ssp. with filter: 50% most abundant and 50% best fitting
library(goeveg)
sel <- ordiselect(dune, mod, ablim = 0.5, fitlim = 0.5)
sel   # 12 species selected

函数的结果对象（包含所选物种的名称）可以放入 select 参数（如上所述）。

自定义素食排序图

Customising vegan ordination plot

plot

r

vegan