NPT_plot: Plot results from nested principal component analysis

In MultiTraits: Analyzing and Visualizing Multidimensional Plant Traits

Plot results from nested principal component analysis

Description

This function creates a visualization of the results from the nested principal component analysis (NPT function) for ecological niche periodicity.

Usage

NPT_plot(pca_obj, group = NULL)

Arguments

pca_obj	An rda object returned by the second-level PCA in the NPT function.
group	A vector or factor specifying the grouping of samples.

Details

The function creates a biplot that includes:

1. Sample points colored by group

2. Species scores represented as arrows

3. Species labels positioned using ggrepel to avoid overlapping

The plot also includes dashed lines at x=0 and y=0, and displays the percentage of variance explained by each principal component on the axes.

Value

A ggplot object representing a biplot of species scores and sample points.

References

1. Winemiller, K. O., Fitzgerald, D. B., Bower, L. M., & Pianka, E. R. (2015). Functional traits, convergent evolution, and periodic tables of niches. Ecology letters, 18(8), 737-751. https://doi.org/10.1111/ele.12462

2. Yu, R., Huang, J., Xu, Y., Ding, Y., & Zang, R. (2020). Plant functional niches in forests across four climatic zones: Exploring the periodic table of niches based on plant functional traits. Frontiers in Plant Science, 11, 841. https://doi.org/10.3389/fpls.2020.00841

Examples

data(PFF)
PFF[,3:20] <- log(PFF[,3:20])
PFF <- na.omit(PFF)
traits_dimension <- list(
  grow = c("SLA","Leaf_area","LDMC","SRL","Leaf_Nmass","Leaf_Pmass","Root_Nmass"),
  survive = c("Height","Leaf_Cmass","Root_Cmass","Leaf_CN","Leaf_NP","Leaf_CP","Root_CN"),
  reproductive = c("SeedMass","FltDate","FltDur")
)
npt_result <- NPT(data = PFF, dimension = traits_dimension)
dev.new() # A window that is too small will interfere with the drawing.
          # Optionally, you can set the drawing window to pop up automatically.
NPT_plot(npt_result$result)
NPT_plot(npt_result$result, PFF$family)

MultiTraits documentation built on April 16, 2025, 9:07 a.m.