Plot phenogram — plot_phenogram • morphospace

Plot phenogram using phylogenetic and morphometric information. Used internally.

plot_phenogram(
  x = NULL,
  y = NULL,
  tree,
  phylo_scores,
  axis,
  lwd.phylo,
  lty.phylo,
  col.phylo,
  cex.nodes,
  pch.nodes,
  col.nodes,
  bg.nodes,
  cex.tips,
  pch.tips,
  col.tips,
  bg.tips,
  points
)

Arguments

x: Optional vector with a non-morphometric variable to be plotted in the x axis.
y: Optional vector with a non-morphometric variable to be plotted in the y axis.
tree: A "phylo" object containing a phylogenetic tree. Tip labels should match the row names from x or y.
phylo_scores: A matrix containing the scores from tips and nodes of the phylogeny provided in tree.
axis: Numeric; the axis to be plotted.
lwd.phylo: Integer; the width of the lines depicting phylogenetic branches.
lty.phylo: Integer; the type of the lines depicting phylogenetic branches.
col.phylo: Numeric; the color of the lines depicting phylogenetic branches.
cex.nodes: Numeric; size of the scatterpoints representing the nodes of the phylogeny.
pch.nodes: Symbol of the scatterpoints representing the nodes of the phylogeny.
col.nodes: Color of the scatterpoints representing the nodes of the phylogeny.
bg.nodes: Background color of the scatterpoints representing the nodes of the phylogeny.
cex.tips: Numeric; size of the scatterpoints representing the tips of the phylogeny.
pch.tips: Symbol of the scatterpoints representing the tips of the phylogeny.
col.tips: Color of the scatterpoints representing the tips of the phylogeny.
bg.tips: Background color of the scatterpoints representing the tips of the phylogeny.
points: Logical; whether to plot the scatter points.

Examples

#load and extract relevant data, packages and information
library(magrittr)
data("tails")
shapes <- tails$shapes
species <- tails$data$species
sp_shapes <- expected_shapes(shapes, species)
tree <- tails$tree
links <- tails$links

#generate basic morphospace, add sampled shapes, species mean shapes, and
#phylogenetic structure
msp <- mspace(shapes, mag = 0.7, axes = c(1,2), cex.ldm = 0,
              plot = FALSE) %>%
  proj_shapes(shapes = shapes, col = c(1:13)[species], pch = 1,
              cex = 0.7) %>%
  proj_shapes(shapes = sp_shapes, pch = 21, bg = 1:13, cex = 2) %>%
  proj_phylogeny(shapes = sp_shapes, tree = tree)
#> Error in plot.xy(xy.coords(x, y), type = type, ...): plot.new has not been called yet

#get node heights
heights <- phytools::nodeHeights(tree)
node_heights <- NULL
for(i in 1:(length(tree$tip.label) + tree$Nnode)) node_heights[i] <- unique(heights[tree$edge == i])

#plot simple phengram
plot(node_heights, msp$projected$phylo_scores[,1])
#> Error in eval(expr, envir, enclos): object 'msp' not found
plot_phenogram(tree = tree, x = node_heights,
               phylo_scores = msp$projected$phylo_scores, axis = 1, lwd.phylo = 1,
               lty.phylo = 1, col.phylo = 1, cex.tips = 1, col.tips = 1,
               pch.tips = 1, cex.nodes = 1, col.nodes = 1, pch.nodes = 1,
               points = TRUE)
#> Error in eval(expr, envir, enclos): object 'msp' not found