monogeneaGM (version 1.1)

tpColorPlot2d: Color-annotated scatter plot with transparency control

Description

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.

Usage

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)

Arguments

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

Details

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.

References

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.

Examples

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)