tpColorPlot3d: Color-annotated three-dimensional scatter plot with...
In monogeneaGM: Geometric Morphometric Analysis of Monogenean Anchors

Description Usage Arguments Details References See Also Examples

This function enhances a three-dimensional scatter plot by enabling transparency control of color annotation. In addition, it provides option for phylogenetic tree superimposition.

1 2	tpColorPlot3d(x, r = 0.005, phylo = FALSE, phy, labcol, xyzlabel = NULL, alpha.set = 0.2, mean.show = FALSE, asp = c(1, 1, 1))

`x`	a matrix with rows representing samples and columns representing three variables of interest, typically principal components
`r`	radius of plotting sphere
`phylo`	if TRUE, coordinates of ancestral nodes from a supplied phylogeny (`phy`) are estimated using `fastAnc` from the `phytools` package, and edges between nodes are joined according to the topology specified in `phy`
`phy`	an object of class `phylo` from the `ape` package
`labcol`	a character vector specifying species colors
`xyzlabel`	a vector of characters specifying the titles for the xyz-axes
`alpha.set`	a constant for controlling degree of transparency (0 for complete transparency; 1 for solid color) of the data points
`mean.show`	if TRUE, the centroids of each species is plotted in solid color
`asp`	a vector specifying the aspect ratio of the xyz axes; the default gives a cube

Transparency control of color-annotated data points reduces visual saturation caused by the use of solid colors for all data points. Guide for choosing optimal value of r: for data range between -0.1 and 0.1, a value of 0.005 should be adequate. If a phylogenetic tree is supplied, it may be superimposed onto the three-dimensional space to allow visualization of evolutionary trajectories.

Khang TF, Soo OYM, Tan WB, Lim LHS. (2016). Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution. PeerJ 4:e1668.

Paradis E, Claude J & Strimmer K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.

Revell LJ. (2012). phytools: An R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3:217-223.

tpColorPlot2d

library(phytools)
library(rgl)

data(ligophorus_shape)
data(ligotree)
data(spcolmap)

#Perform PCA of shape data for dorsal anchors and make 2D plots
pcashape <- pca2d(ligophorus_shape[,23:44], labcol=spcolmap$color,
phylo=TRUE, phy=ligotree, genus="L. ", bound.y=c(-0.08, 0.1),
bound.x1=c(-0.2,0.2), bound.x2 = c(-0.2,0.2))

#Check for proportion of variation explained by each PC
summary(pcashape$pca)

#A closer look with 3D plot
tpColorPlot3d(pcashape$scores[,3:1], r=0.005, phylo=TRUE, phy=ligotree, labcol=spcolmap$color,
xyzlabel=c("PC3 (8%)","PC2 (10%)","PC1 (61%)"), mean.show=TRUE)