R/picknplot.shape.r
In EmSherratt/geomorph: Geometric Morphometric Analyses of 2D/3D Landmark Data
Defines functions
picknplot.shape
Documented in
picknplot.shape
#' Pick points in geomorph scatterplots to visualize shape variation
#'
#' Function plots the shape corresponding to a clicked point in the area of a geomorph plot
#'
#' THIS FUNCTION IS A BIT EXPERIMENTAL!
#'
#' This function recycles plots generated by \code{\link{plot.gm.prcomp}}, \code{\link{plot.procD.lm}},
#' \code{\link{plot.pls}}, or \code{\link{plotAllometry}}, and makes them interactive to visualize shape variation by selecting one or more points in morphospace.
#' The function uses \code{\link{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 \code{\link{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 \code{\link{plot.gm.prcomp}}. The function is limited in terms of the options for
#' \code{\link{plotRefToTarget}} (because of the complexity of graphics); using \code{\link{shape.predictor}} and \code{\link{plotRefToTarget}}, directly,
#' will always offer more flexibility.
#'
#' IF YOU EXPERIENCE AN ERROR, please use \code{\link{shape.predictor}} and \code{\link{plotRefToTarget}}, directly. (But please alert the
#' geomorph package maintainer.)
#'
#'
#' @param x a geomorph plot object of class plot.gm.prcomp, plot.procD.lm, plot.pls, or plotAllometry
#' @param ... other arguments passed to \code{\link{plotRefToTarget}}
#' @return A list with the following components:
#' \item{points}{A list with the xy coordinates of the selected points.}
#' \item{shapes}{A list with the corresponding estimated shapes.}
#' @keywords visualization
#' @export
#' @author Antigoni Kaliontzopoulou, Emma Sherratt, & Michael Collyer
#' @seealso \code{\link{shape.predictor}}, \code{\link{plotRefToTarget}}
#' @seealso \code{\link[rgl]{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$Csize)
#' # PLS.plot = plot(PLS)
#' # picknplot.shape(PLS.plot)
picknplot.shape <- function(x, ...){
if(!inherits(x, c("plot.gm.prcomp", "plot.procD.lm", "plotAllometry", "plot.pls"))){
stop("Class of plot object not compatible with picknplot.shape. \nPlease see the help file for allowed plot objects\n",
call. = FALSE)
}
do.call(plot, x$plot.args)
if(!is.null(x$phylo)){
phylo.par <- x$phylo$phylo.par
phy <- x$phylo$phy
phy.pcdata <- x$phylo$phy.pcdata
for (i in 1:nrow(phy$edge)) {
dt.xy <- xy.coords(phy.pcdata[phy$edge[i,], ])
plot.xy(dt.xy, type="l", col = phylo.par$edge.color,
lwd = phylo.par$edge.width, lty = phylo.par$edge.lty)
}
plot.xy(xy.coords(phy.pcdata[1:length(phy$tip),]), type="p")
plot.xy(xy.coords(phy.pcdata[(length(phy$tip)+1):nrow(phy.pcdata),]), type="p",
pch = phylo.par$node.pch, cex = phylo.par$node.cex, bg = phylo.par$node.bg)
}
continue <- "y"
p = 1
picked.pts <- picked.shapes <- list()
prt.args <- list(...)
prt.args.nms <- c("mesh", "outline", "method", "mag",
"links", "label", "axes", "gridPar", "useRefPts")
prt.args.pos <- intersect(names(prt.args), prt.args.nms)
# plot.args currently not used but could be in the future
# adding a phylogeny currently has no plotting options
prt.args <- prt.args[prt.args.pos]
if(is.null(prt.args$method)) prt.args$method <- "TPS"
if(prt.args$method == "surface") {
cat("method = 'surface' is not possible.",
"\n Use shape.predictor and plotRefToTarget for this option.\n")
}
if(!inherits(x, "plot.pls")) {
type <- "PC"
if(is.null(x$GM$A)) A1 <- x$GM$fitted else
A1 <- x$GM$A
if(is.null(A1)) stop("No shape data provided\n", call. = FALSE)
A2 <- NULL
if(!is.null(x$PredLine)) {
if(!is.null(x$CAC)) {
if(identical(x$plot.args$y, x$CAC)) {
A1 <- A1 + x$GM$residuals
type <- "regression2"
}
}
if(identical(x$plot.args$y, x$PredLine) || identical(x$plot.args$y, x$RegScore))
type <- "regression2"
if(length(dim(A1)) != 3) stop("No shape data provided\n", call. = FALSE)
}
} else {
type <- "PLS"
A1 <- x$A1
A2 <- x$A2
if(length(dim(A1)) != 3) A1 <- NULL
if(length(dim(A2)) != 3) A2 <- NULL
if(is.null(A1) && is.null(A2)) stop("No shape data provided\n", call. = FALSE)
if(is.null(A1) && !is.null(A2)) type <- "regression2"
if(!is.null(A1) && is.null(A2)) type <- "regression1"
if(type == "regression2") {
A1 <- A2
A2 <- NULL
}
}
if(!is.null(A1) && dim(A1)[2] == 3) {
cat("Only method = 'points' or 'vector' can be used for 3D data in this function.",
"\nSwitching to method = 'points'. Use shape.predictor and plotRefToTarget for more options.\n\n")
prt.args$method <- "points"
}
if(!is.null(A1) && dim(A1)[2] != 3 && !is.null(A2) && dim(A2)[2] == 3) {
cat("Only method = 'points' or 'vector' can be used for 3D data in this function.",
"\nSwitching to method = 'points'. Use shape.predictor and plotRefToTarget for more options.\n\n")
prt.args$method <- "points"
}
while(continue == "y"){
cat("Pick a point in the shape space", "\n")
picked.pts[[p]] <- unlist(locator(n = 1, type = "p", pch = 20, col = "red", cex = 1))
cat("Picked point coordinates are:", "\n")
cat(picked.pts[[p]], "\n")
if(type == "PC") {
X <- as.matrix(cbind(x$plot.args$x, x$plot.args$y))
rownames(X) <- names(x$plot.args$x)
if(!is.null(x$Pcov)) X <- fast.solve(x$Pcov) %*% X
picked.shapes[[p]] <- shape.predictor(A1, X,
pred1 = picked.pts[[p]])$pred1
}
if(type == "regression2") {
h <- picked.pts[[p]][2]
abline(h = h, col = "red")
X <- as.matrix(x$plot.args$y)
rownames(X) <- names(x$plot.args$x)
if(!is.null(x$Pcov)) X <- fast.solve(x$Pcov) %*% X
picked.shapes[[p]] <- shape.predictor(A1, X,
pred1 = h)$pred1
}
if(type == "regression1") {
v <- picked.pts[[p]][1]
abline(v = v, col = "red")
X <- as.matrix(x$plot.args$x)
rownames(X) <- names(x$plot.args$x)
if(!is.null(x$Pcov)) X <- fast.solve(x$Pcov) %*% X
picked.shapes[[p]] <- shape.predictor(A1, X,
pred1 = v)$pred1
}
if(type == "PLS") {
X <- as.matrix(cbind(x$plot.args$x, x$plot.args$y))
rownames(X) <- names(x$plot.args$x)
if(!is.null(x$Pcov)) X <- fast.solve(x$Pcov) %*% X
picked.shapes[[p]] <- list(P1 = shape.predictor(A1, X,
pred1 = picked.pts[[p]])$pred1,
P2 = shape.predictor(A2, X,
pred1 = picked.pts[[p]])$pred1)
}
if(type == "PC" || type == "regression1" || type == "regression2") {
if (dim(A1)[2] == 2) {
prt.args$M1 <- cbind(mshape(A1), 0)
prt.args$M2 <- cbind(picked.shapes[[p]], 0)
class(prt.args$M2) <- "predshape.k2"
view3d(phi = 0, fov = 30, interactive = FALSE)
do.call(plotRefToTarget, prt.args)
}
if (dim(A1)[2] == 3){
prt.args$M1 <- mshape(A1)
prt.args$M2 <- picked.shapes[[p]]
class(prt.args$M2) <- "predshape.k3"
if(prt.args$method == "TPS"){
view3d(phi = 0, fov = 30, interactive = FALSE)
} else {
view3d(phi = 0, fov = 30, interactive = TRUE)
}
do.call(plotRefToTarget, prt.args)
}
}
if(type == "PLS") {
if (dim(A1)[2] == 2) {
prt.args$M1 <- cbind(mshape(A1), 0)
prt.args$M2 <- cbind(picked.shapes[[p]][[1]], 0)
class(prt.args$M2) <- "predshape.k2"
view3d(phi = 0, fov = 30, interactive = FALSE)
mfrow3d(1, 2)
do.call(plotRefToTarget, prt.args)
}
if (dim(A1)[2] == 3){
prt.args$main = "PLS Block 1"
prt.args$M1 <- mshape(A1)
prt.args$M2 <- picked.shapes[[p]][[1]]
class(prt.args$M2) <- "predshape.k3"
if(prt.args$method == "TPS"){
open3d()
mfrow3d(1, 2)
} else {
open3d()
mfrow3d(1, 2)
}
do.call(plotRefToTarget, prt.args)
}
if (dim(A2)[2] == 2) {
prt.args$main = "PLS Block 2"
prt.args$M1 <- cbind(mshape(A2), 0)
prt.args$M2 <- cbind(picked.shapes[[p]][[2]], 0)
class(prt.args$M2) <- "predshape.k2"
do.call(plotRefToTarget, prt.args)
}
if (dim(A2)[2] == 3){
prt.args$main = "PLS Block 2"
prt.args$M1 <- mshape(A2)
prt.args$M2 <- picked.shapes[[p]][[2]]
class(prt.args$M2) <- "predshape.k3"
do.call(plotRefToTarget, prt.args)
}
}
ans <- readline("Save deformation grid as png file (y/n)? ")
if(ans=="y") {
file.name <- readline("Please provide file name for saving deformation grid (without quotes) ")
rgl.snapshot(filename = file.name)
}
if(ans=="n"){
try(rgl.close(), silent=T)
}
continue <- readline("Do you want to pick another point (y/n)? ")
p = p + 1
}
out <- list(points = picked.pts, shapes = picked.shapes)
invisible(out)
}
EmSherratt/geomorph documentation built on June 24, 2022, 11:05 p.m.
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Defines functions picknplot.shape
Documented in picknplot.shape
#' Pick points in geomorph scatterplots to visualize shape variation
#'
#' Function plots the shape corresponding to a clicked point in the area of a geomorph plot
#'
#' THIS FUNCTION IS A BIT EXPERIMENTAL!
#'
#' This function recycles plots generated by \code{\link{plot.gm.prcomp}}, \code{\link{plot.procD.lm}},
#' \code{\link{plot.pls}}, or \code{\link{plotAllometry}}, and makes them interactive to visualize shape variation by selecting one or more points in morphospace.
#' The function uses \code{\link{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 \code{\link{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 \code{\link{plot.gm.prcomp}}. The function is limited in terms of the options for
#' \code{\link{plotRefToTarget}} (because of the complexity of graphics); using \code{\link{shape.predictor}} and \code{\link{plotRefToTarget}}, directly,
#' will always offer more flexibility.
#'
#' IF YOU EXPERIENCE AN ERROR, please use \code{\link{shape.predictor}} and \code{\link{plotRefToTarget}}, directly. (But please alert the
#' geomorph package maintainer.)
#'
#'
#' @param x a geomorph plot object of class plot.gm.prcomp, plot.procD.lm, plot.pls, or plotAllometry
#' @param ... other arguments passed to \code{\link{plotRefToTarget}}
#' @return A list with the following components:
#' \item{points}{A list with the xy coordinates of the selected points.}
#' \item{shapes}{A list with the corresponding estimated shapes.}
#' @keywords visualization
#' @export
#' @author Antigoni Kaliontzopoulou, Emma Sherratt, & Michael Collyer
#' @seealso \code{\link{shape.predictor}}, \code{\link{plotRefToTarget}}
#' @seealso \code{\link[rgl]{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)
picknplot.shape <- function(x, ...){
if(!inherits(x, c("plot.gm.prcomp", "plot.procD.lm", "plotAllometry", "plot.pls"))){
stop("Class of plot object not compatible with picknplot.shape. \nPlease see the help file for allowed plot objects\n",
call. = FALSE)
}
do.call(plot, x$plot.args)
if(!is.null(x$phylo)){
phylo.par <- x$phylo$phylo.par
phy <- x$phylo$phy
phy.pcdata <- x$phylo$phy.pcdata
for (i in 1:nrow(phy$edge)) {
dt.xy <- xy.coords(phy.pcdata[phy$edge[i,], ])
plot.xy(dt.xy, type="l", col = phylo.par$edge.color,
lwd = phylo.par$edge.width, lty = phylo.par$edge.lty)
}
plot.xy(xy.coords(phy.pcdata[1:length(phy$tip),]), type="p")
plot.xy(xy.coords(phy.pcdata[(length(phy$tip)+1):nrow(phy.pcdata),]), type="p",
pch = phylo.par$node.pch, cex = phylo.par$node.cex, bg = phylo.par$node.bg)
}
continue <- "y"
p = 1
picked.pts <- picked.shapes <- list()
prt.args <- list(...)
prt.args.nms <- c("mesh", "outline", "method", "mag",
"links", "label", "axes", "gridPar", "useRefPts")
prt.args.pos <- intersect(names(prt.args), prt.args.nms)
# plot.args currently not used but could be in the future
# adding a phylogeny currently has no plotting options
prt.args <- prt.args[prt.args.pos]
if(is.null(prt.args$method)) prt.args$method <- "TPS"
if(prt.args$method == "surface") {
cat("method = 'surface' is not possible.",
"\n Use shape.predictor and plotRefToTarget for this option.\n")
}
if(!inherits(x, "plot.pls")) {
type <- "PC"
if(is.null(x$GM$A)) A1 <- x$GM$fitted else
A1 <- x$GM$A
if(is.null(A1)) stop("No shape data provided\n", call. = FALSE)
A2 <- NULL
if(!is.null(x$PredLine)) {
if(!is.null(x$CAC)) {
if(identical(x$plot.args$y, x$CAC)) {
A1 <- A1 + x$GM$residuals
type <- "regression2"
}
}
if(identical(x$plot.args$y, x$PredLine) || identical(x$plot.args$y, x$RegScore))
type <- "regression2"
if(length(dim(A1)) != 3) stop("No shape data provided\n", call. = FALSE)
}
} else {
type <- "PLS"
A1 <- x$A1
A2 <- x$A2
if(length(dim(A1)) != 3) A1 <- NULL
if(length(dim(A2)) != 3) A2 <- NULL
if(is.null(A1) && is.null(A2)) stop("No shape data provided\n", call. = FALSE)
if(is.null(A1) && !is.null(A2)) type <- "regression2"
if(!is.null(A1) && is.null(A2)) type <- "regression1"
if(type == "regression2") {
A1 <- A2
A2 <- NULL
}
}
if(!is.null(A1) && dim(A1)[2] == 3) {
cat("Only method = 'points' or 'vector' can be used for 3D data in this function.",
"\nSwitching to method = 'points'. Use shape.predictor and plotRefToTarget for more options.\n\n")
prt.args$method <- "points"
}
if(!is.null(A1) && dim(A1)[2] != 3 && !is.null(A2) && dim(A2)[2] == 3) {
cat("Only method = 'points' or 'vector' can be used for 3D data in this function.",
"\nSwitching to method = 'points'. Use shape.predictor and plotRefToTarget for more options.\n\n")
prt.args$method <- "points"
}
while(continue == "y"){
cat("Pick a point in the shape space", "\n")
picked.pts[[p]] <- unlist(locator(n = 1, type = "p", pch = 20, col = "red", cex = 1))
cat("Picked point coordinates are:", "\n")
cat(picked.pts[[p]], "\n")
if(type == "PC") {
X <- as.matrix(cbind(x$plot.args$x, x$plot.args$y))
rownames(X) <- names(x$plot.args$x)
if(!is.null(x$Pcov)) X <- fast.solve(x$Pcov) %*% X
picked.shapes[[p]] <- shape.predictor(A1, X,
pred1 = picked.pts[[p]])$pred1
}
if(type == "regression2") {
h <- picked.pts[[p]][2]
abline(h = h, col = "red")
X <- as.matrix(x$plot.args$y)
rownames(X) <- names(x$plot.args$x)
if(!is.null(x$Pcov)) X <- fast.solve(x$Pcov) %*% X
picked.shapes[[p]] <- shape.predictor(A1, X,
pred1 = h)$pred1
}
if(type == "regression1") {
v <- picked.pts[[p]][1]
abline(v = v, col = "red")
X <- as.matrix(x$plot.args$x)
rownames(X) <- names(x$plot.args$x)
if(!is.null(x$Pcov)) X <- fast.solve(x$Pcov) %*% X
picked.shapes[[p]] <- shape.predictor(A1, X,
pred1 = v)$pred1
}
if(type == "PLS") {
X <- as.matrix(cbind(x$plot.args$x, x$plot.args$y))
rownames(X) <- names(x$plot.args$x)
if(!is.null(x$Pcov)) X <- fast.solve(x$Pcov) %*% X
picked.shapes[[p]] <- list(P1 = shape.predictor(A1, X,
pred1 = picked.pts[[p]])$pred1,
P2 = shape.predictor(A2, X,
pred1 = picked.pts[[p]])$pred1)
}
if(type == "PC" || type == "regression1" || type == "regression2") {
if (dim(A1)[2] == 2) {
prt.args$M1 <- cbind(mshape(A1), 0)
prt.args$M2 <- cbind(picked.shapes[[p]], 0)
class(prt.args$M2) <- "predshape.k2"
view3d(phi = 0, fov = 30, interactive = FALSE)
do.call(plotRefToTarget, prt.args)
}
if (dim(A1)[2] == 3){
prt.args$M1 <- mshape(A1)
prt.args$M2 <- picked.shapes[[p]]
class(prt.args$M2) <- "predshape.k3"
if(prt.args$method == "TPS"){
view3d(phi = 0, fov = 30, interactive = FALSE)
} else {
view3d(phi = 0, fov = 30, interactive = TRUE)
}
do.call(plotRefToTarget, prt.args)
}
}
if(type == "PLS") {
if (dim(A1)[2] == 2) {
prt.args$M1 <- cbind(mshape(A1), 0)
prt.args$M2 <- cbind(picked.shapes[[p]][[1]], 0)
class(prt.args$M2) <- "predshape.k2"
view3d(phi = 0, fov = 30, interactive = FALSE)
mfrow3d(1, 2)
do.call(plotRefToTarget, prt.args)
}
if (dim(A1)[2] == 3){
prt.args$main = "PLS Block 1"
prt.args$M1 <- mshape(A1)
prt.args$M2 <- picked.shapes[[p]][[1]]
class(prt.args$M2) <- "predshape.k3"
if(prt.args$method == "TPS"){
open3d()
mfrow3d(1, 2)
} else {
open3d()
mfrow3d(1, 2)
}
do.call(plotRefToTarget, prt.args)
}
if (dim(A2)[2] == 2) {
prt.args$main = "PLS Block 2"
prt.args$M1 <- cbind(mshape(A2), 0)
prt.args$M2 <- cbind(picked.shapes[[p]][[2]], 0)
class(prt.args$M2) <- "predshape.k2"
do.call(plotRefToTarget, prt.args)
}
if (dim(A2)[2] == 3){
prt.args$main = "PLS Block 2"
prt.args$M1 <- mshape(A2)
prt.args$M2 <- picked.shapes[[p]][[2]]
class(prt.args$M2) <- "predshape.k3"
do.call(plotRefToTarget, prt.args)
}
}
ans <- readline("Save deformation grid as png file (y/n)? ")
if(ans=="y") {
file.name <- readline("Please provide file name for saving deformation grid (without quotes) ")
rgl.snapshot(filename = file.name)
}
if(ans=="n"){
try(rgl.close(), silent=T)
}
continue <- readline("Do you want to pick another point (y/n)? ")
p = p + 1
}
out <- list(points = picked.pts, shapes = picked.shapes)
invisible(out)
}
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