tpColorPlot2d: Color-annotated scatter plot with transparency control
In monogeneaGM: Geometric Morphometric Analysis of Monogenean Anchors

Description Usage Arguments Details Author(s) References Examples

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

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tpColorPlot2d(x, labcol = "", xlab = "", ylab = "", tit = "",
  circlesize = rep(1.5, nrow(x)), tpfac = c(60, 255), xbound = NULL,
  ybound = NULL, centroid = FALSE, phylo = FALSE, phy, pointscale = 1)

`x`	a two-column matrix with rownames (usually, the species names)
`labcol`	a character vector specifying species colors
`xlab`	title for the x-axis
`ylab`	title for the y-axis
`tit`	title for the plot
`circlesize`	a numeric vector that controls the centroid symbol size; defaults to 1 if `centroid = FALSE`
`tpfac`	a numeric vector specifying the transparency level (0 to 255) for individual data points and the label mean
`xbound`	range of values on the x-axis
`ybound`	range of values on the y-axis
`centroid`	if TRUE, plots the centroid for each species
`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
`pointscale`	a constant for controlling the size of the plotted ancestral nodes

Transparency control of color-annotated data points reduces visual saturation caused by the use of solid colours, thus allowing species centroids to be accentuated in the plot. In addition, if a user-supplied phylogeny is given, it is superimposed onto the plot. This function depends on the phytools (Revell, 2012) and ape (Paradis et al., 2004) packages.

Tsung Fei Khang tfkhang@um.edu.my

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.

data(pwed_pd)
data(spcolmap)

pwed_pd_list <- matrix2list.2(pwed_pd)
lm1 <- c("V1_3","V1_5")

#scatter plot of LM1-LM3 length against LM1-LM5 length for the ventral anchors
tpColorPlot2d(pwed_pd[,colnames(pwed_pd) %in% lm1], labcol=spcolmap$color,
xlab=expression(paste("V1_3 ", "(", italic(mu),"m", ")")),
ylab=expression(paste("V1_5 ", "(", italic(mu),"m", ")")), centroid=TRUE)