monogeneaGM (version 1.1)

hsplot: Scatter plot with marginal histograms

Description

This function creates a scatter plot that is augmented with marginal histograms (with smoothed splines) on the x and y-axes.

Usage

hsplot(dat, seqx, seqy, ybound, xbound, y.label = "", x.label = "", labcol, type = "ru", sep1, sep2, phylo = FALSE, phy, pointscale = 1.5, supp.hist.y = FALSE, supp.hist.x = FALSE, y.axis.label = TRUE, x.axis.label = TRUE, addline = NULL)

Arguments

dat

a matrix with rows representing species samples and two columns representing the variables of interest (typically a selected principal component of size and shape variables)

seqx

range of values on the x-axis, for histogram plotting

seqy

range of values on the y-axis, for histogram plotting

ybound

range of values on the y-axis

xbound

range of values on the x-axis

y.label

title for y-axis

x.label

title for x-axis

labcol

a character vector giving the color annotation for species names in alphabetical order

type

a character that controls where the marginal histograms are located: right-up ("ru"), left-up ("lu"), left-down ("ld"), right-down ("rd")

sep1

tick mark separation for x-axis

sep2

tick mark separation for y-axis

phylo

if TRUE, the centroids of species are joined into a tree-like object corresponding to their phylogeny given in phy

phy

a tree object of class phylo

pointscale

a constant specifying the symbol size of the centroids

supp.hist.y

if TRUE, suppresses the plotting of marginal histogram at the y-axis

supp.hist.x

if TRUE, suppresses the plotting of marginal histogram at the x-axis

y.axis.label

if FALSE, suppresses the y-axis title

x.axis.label

if FALSE, suppresses the x-axis title

addline

an optional numeric vector of length two specifying the intercept and slope of linear line

Details

This function is similar to tpColorPlot2d, and is mainly useful for its additional option for visualising the marginal distributions. The ape and phytools packages are required.

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

library(phytools)

data(pwed_pd)
data(ligotree)
data(spcolmap)

#principal component analysis of size variables from ventral and dorsal anchors
pca2d_pwedv <- pca2d(pwed_pd[,1:55], sgn=-1, labcol=spcolmap$color,
phylo=TRUE, phy=ligotree, genus="L. ", bound.y=c(-0.2, 0.2),
bound.x1=c(-0.2,0.2), bound.x2 = c(-0.2,0.2))
pca2d_pwedd <- pca2d(pwed_pd[,56:110], sgn=-1, labcol=spcolmap$color,
phylo=TRUE, phy=ligotree, genus="L. ", bound.y=c(-0.2, 0.2),
bound.x1=c(-0.2,0.2), bound.x2 = c(-0.2,0.2))

#comparing size PC1 between ventral and dorsal anchors
hsplot(cbind(pca2d_pwedv$scores[,1], pca2d_pwedd$scores[,1]),
seqx=seq(-0.2,0.15,0.01), seqy=seq(-0.2,0.15,0.01),
xbound=c(-0.2,0.15), ybound=c(-0.2,0.15), y.label="Dorsal size PC1",
x.label="Ventral size PC1", labcol=spcolmap$color, type="ru",
sep1=0.1, sep2=0.1, phylo=FALSE, addline=c(0,1))