picknplot.shape: Pick points in geomorph scatterplots to visualize shape...

In EmSherratt/geomorph: Geometric Morphometric Analyses of 2D/3D Landmark Data

Pick points in geomorph scatterplots to visualize shape variation

Description

Function plots the shape corresponding to a clicked point in the area of a geomorph plot

Usage

picknplot.shape(x, ...)

Arguments

x	a geomorph plot object of class plot.gm.prcomp, plot.procD.lm, plot.pls, or plotAllometry
...	other arguments passed to plotRefToTarget

Details

THIS FUNCTION IS A BIT EXPERIMENTAL!

This function recycles plots generated by plot.gm.prcomp, plot.procD.lm, plot.pls, or plotAllometry, and makes them interactive to visualize shape variation by selecting one or more points in morphospace. The function uses shape.predictor to estimate the shape corresponding to the selected point(s) based on the prediction underlying the scatterplot, and it plots the estimated shape as compared to the consensus landmark configuration using plotRefToTarget. The user is then prompted as to whether the plotted shape is to be saved as a png file, in which case the name of the file needs to be provided (without quotation marks). Interactive plots are at present available for plots produced by plot.gm.prcomp. The function is limited in terms of the options for plotRefToTarget (because of the complexity of graphics); using shape.predictor and plotRefToTarget, directly, will always offer more flexibility.

IF YOU EXPERIENCE AN ERROR, please use shape.predictor and plotRefToTarget, directly. (But please alert the geomorph package maintainer.)

Value

A list with the following components:

points	A list with the xy coordinates of the selected points.
shapes	A list with the corresponding estimated shapes.

Author(s)

Antigoni Kaliontzopoulou, Emma Sherratt, & Michael Collyer

See Also

shape.predictor, plotRefToTarget

rgl-package (used in 3D plotting)

Examples

### Because picknplot requires user decisions, the following examples
### are not run (but can be with removal of #s)

# 2d
# data(plethodon) 
# Y.gpa <- gpagen(plethodon$land)
# pleth.pca <- gm.prcomp(Y.gpa$coords)
# pleth.pca.plot <- plot(pleth.pca)
# picknplot.shape(pleth.pca.plot) 
# May change arguments for plotRefToTarget
# picknplot.shape(plot(pleth.pca), method = "points", mag = 3, 
# links=plethodon$links)

# 2d with phylogeny
# data(plethspecies) 
# Y.gpa <- gpagen(plethspecies$land)
# gps <- as.factor(c(rep("gp1", 5), rep("gp2", 4))) # Two random groups
# pleth.phylo <- gm.prcomp(Y.gpa$coords, plethspecies$phy)
# pleth.phylomorphospace <- plot(pleth.phylo, phylo = TRUE, cex = 2, 
# pch = 22, bg = gps, phylo.par = list(edge.color = "blue", 
# edge.width = 2, edge.lty = 2,
# node.pch = 22, node.bg = "black"))
# links.species <- plethodon$links[-11,]
# links.species[11, 1] <- 11
# picknplot.shape(pleth.phylomorphospace, method = "points", 
# links = links.species)

# 2d allometry 
# gdf <- geomorph.data.frame(Y.gpa, site = plethodon$site, 
# species = plethodon$species) 
# fit <- procD.lm(coords ~ log(Csize), data=gdf, iter=0, 
# print.progress = FALSE)
# Predline
# PA <- plotAllometry(fit, size = gdf$Csize, logsz = TRUE, 
# method = "PredLine", pch = 19)
# picknplot.shape(PA)

# 3d and two-b-pls
# data("scallops")
# Y.gpa <- gpagen(scallops$coorddata, curves = scallops$curvslide, 
#              surfaces = scallops$surfslide)
# PLS <- two.b.pls(Y.gpa$coords, Y.gpa$Csize)
# PLS.plot = plot(PLS)
# picknplot.shape(PLS.plot)

EmSherratt/geomorph documentation built on June 24, 2022, 11:05 p.m.