PTMN_plot: Plot Plant Trait Multilayer Networks (PTMN)

In MultiTraits: Analyzing and Visualizing Multidimensional Plant Traits

Plot Plant Trait Multilayer Networks (PTMN)

Description

This function creates visualizations of plant trait multilayer networks (PTMNs) constructed using the PTMN framework. PTMNs systematically integrate multilayer network theory with plant functional trait analysis, enabling quantitative assessments of trait relationships across plant organs and functional systems.

Usage

PTMN_plot(
  data,
  style = 1,
  vertex.size = 15,
  show.labels = TRUE,
  vertex.label.cex = 0.7,
  vertex.label.dist = 0.2,
  edge.width = 2,
  vertex.label.font = 2,
  node.alpha = 1,
  module.alpha = 0.3,
  show.legend = TRUE,
  legend.pos = "bottomright",
  legend.cex = 1,
  legend.pt.size = 2.5,
  x.intersp = 2,
  y.intersp = 2,
  title.font = 2,
  title.cex = 1.2
)

Arguments

data	A data frame containing the PTMN edge list with columns: node.from, node.to, layer.from, layer.to. This should be the output from the PTMN function.
style	Integer specifying the layout style. Options are: 1 - Standard network layout with cross-layer module highlighting (default) 2 - Circular layout with nodes arranged by layer
vertex.size	Numeric value controlling the size of network nodes (vertices). Default is 15.
show.labels	Logical indicating whether to display node labels. Default is TRUE.
vertex.label.cex	Numeric value controlling the size of vertex labels. Default is 0.7.
vertex.label.dist	Numeric value controlling the distance of labels from vertices. Default is 0.2.
edge.width	Numeric value controlling the width of network edges. Default is 2.
vertex.label.font	Integer specifying the font style for vertex labels (1=plain, 2=bold, 3=italic, 4=bold italic). Default is 2.
node.alpha	Numeric value between 0 and 1 controlling the transparency of nodes. Default is 1 (opaque).
module.alpha	Numeric value between 0 and 1 controlling the transparency of module highlighting. Default is 0.3.
show.legend	Logical indicating whether to display the layer legend. Default is TRUE.
legend.pos	Character string specifying legend position. Options include "bottomright", "bottomleft", "topright", "topleft". Default is "bottomright".
legend.cex	Numeric value controlling the size of legend text. Default is 1.
legend.pt.size	Numeric value controlling the size of legend symbols. Default is 2.5.
x.intersp	Numeric value controlling horizontal spacing in legend. Default is 2.
y.intersp	Numeric value controlling vertical spacing in legend. Default is 2.
title.font	Integer specifying the font style for legend title. Default is 2 (bold).
title.cex	Numeric value controlling the size of legend title. Default is 1.2.

Details

The PTMN visualization distinguishes between intralayer edges (black lines) showing relationships between traits within the same organ or functional system, and interlayer edges (red lines) representing interactions between traits in different layers. Each layer corresponds to specific functional or structural units such as individual plant organs (leaves, stems, roots) or functional systems.

In style 1, cross-layer modules are highlighted with shaded areas, representing tightly connected functional groups that span multiple layers. In style 2, the circular layout arranges nodes by layer in a circular pattern, making layer organization more visually apparent.

Node colors are automatically assigned based on layer membership using the "ggsci::nrc_npg" color palette, ensuring visual distinction between different functional layers.

Value

No return value. This function is called for its side effect of creating a network plot.

See Also

PTMN for constructing plant trait multilayer networks

Examples

## Not run: 
data(forest_invader_tree)
data(forest_invader_traits)
traits <- forest_invader_traits[, 6:73]
layers <- list(
  shoot_dynamics = c("LeafDuration", "LeafFall50", "LeafRate_max",
                     "Chl_shade50", "LAgain", "FallDuration",
                     "LeafOut", "Chl_sun50", "EmergeDuration",
                     "LeafTurnover"),
  leaf_structure = c("PA_leaf", "Mass_leaf", "Lifespan_leaf",
                     "Thick_leaf", "SLA", "Lobe", "LDMC",
                     "Stomate_size", "Stomate_index"),
  leaf_metabolism = c("J_max", "Vc_max", "Asat_area", "CC_mass",
                      "LSP", "AQY", "CC_area", "Rd_area",
                      "Asat_mass", "WUE", "Rd_mass", "PNUE"),
  leaf_chemistry = c("N_area", "Chl_area", "DNA", "Phenolics",
                     "Cellulose", "N_mass", "N_litter", "Chl_ab",
                     "Chl_mass", "N_res", "C_litter", "C_area",
                     "C_mass", "Ash", "Lignin", "Solubles",
                     "Decomp_leaf", "Hemi"),
  root = c("NPP_root", "SS_root", "SRL", "RTD", "RDMC",
           "NSC_root", "Decomp_root", "Starch_root",
           "C_root", "N_root", "Lignin_root"),
  stem = c("Latewood_diam", "Metaxylem_diam", "Earlywood_diam",
           "NSC_stem", "Vessel_freq", "SS_stem", "Cond_stem",
           "Starch_stem")
)
graph <- PTMN(traits, layers_list = layers, method = "pearson")
PTMN_plot(graph, style = 1, vertex.size = 8,
          vertex.label.cex = 0.5, edge.width = 2,
          show.legend = FALSE)

## End(Not run)

MultiTraits documentation built on March 22, 2026, 9:06 a.m.