hsplot: Scatter plot with marginal histograms
In monogeneaGM: Geometric Morphometric Analysis of Monogenean Anchors

Description Usage Arguments Details Author(s) References Examples

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

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)

`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

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.

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.

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))