3D Plots in R

#IRIS 3D Plot

#install.packages("plot3D")
library("plot3D")
data(iris)
head(iris)

# x, y and z coordinates
x <- sep.l <- iris$Sepal.Length
y <- pet.l <- iris$Petal.Length
z <- sep.w <- iris$Sepal.Width

#Scatter plots
scatter3D(x, y, z, ..., colvar = z, col = NULL, add = FALSE)
text3D(x, y, z, labels, colvar = NULL, add = FALSE)
points3D(x, y, z, ...)
lines3D(x, y, z, ...)
scatter2D(x, y, colvar = NULL, col = NULL, add = FALSE)
text2D(x, y, labels, colvar = NULL, col = NULL, add = FALSE)

scatter3D(x, y, z, clab = c("Sepal", "Width (cm)"))

scatter3D(x, y, z, colvar = NULL, col = "blue",

pch = 19, cex = 0.5)

#Change the type of the box around the plot

# full box
scatter3D(x, y, z, bty = "f", colkey = FALSE, main ="bty= 'f'")
# back panels and grid lines are visible
scatter3D(x, y, z, bty = "b2", colkey = FALSE, main ="bty= 'b2'" )

# grey background with white grid lines

scatter3D(x, y, z, bty = "g", colkey = FALSE, main ="bty= 'g'")
# User defined
scatter3D(x, y, z, pch = 18, bty = "u", colkey = FALSE,
main ="bty= 'u'", col.panel ="steelblue", expand =0.4,
col.grid = "darkblue")

#Color palettes
# gg.col: ggplot2 like color
scatter3D(x, y, z, bty = "g", pch = 18, col = gg.col(100))
# ramp.col: custom palettes
scatter3D(x, y, z, bty = "g", pch = 18,
col = ramp.col(c("blue", "yellow", "red")) )
#Change the color by groups
scatter3D(x, y, z, bty = "g", pch = 18,
col.var = as.integer(iris$Species),
col = c("#1B9E77", "#D95F02", "#7570B3"),
pch = 18, ticktype = "detailed",
colkey = list(at = c(2, 3, 4), side = 1,
addlines = TRUE, length = 0.5, width = 0.5,
labels = c("setosa", "versicolor", "virginica")) )

#Change the position of the legend

# Bottom colkey
scatter3D(x, y, z, bty = "g",
colkey = list(side = 1, length = 0.5))

#3D viewing direction

scatter3D(x, y, z, theta = 15, phi = 20)

scatter3D(x, y, z, phi = 0, bty ="g")

#Titles and axis labels

scatter3D(x, y, z, pch = 18, theta = 20, phi = 20,
main = "Iris data", xlab = "Sepal.Length",
ylab ="Petal.Length", zlab = "Sepal.Width")

#Tick marks and labels

scatter3D(x, y, z, phi = 0, bty = "g",
pch = 20, cex = 2, ticktype = "detailed")

#Add points and text to an existing plot

# The functions below can be used:
#
# scatter3D(x, y, z,…, add = TRUE): Adds points
# text3D(x, y, z, labels, …, add = TRUE): Adds texts
# Add points to an existing plot:
# Create a scatter plot
scatter3D(x, y, z, phi = 0, bty = "g",
pch = 20, cex = 2, ticktype = "detailed")
# Add another point (black color)
scatter3D(x = 7, y = 3, z = 3.5, add = TRUE, colkey = FALSE,
pch = 18, cex = 3, col = "black")

# Add texts to an existing plot:

# Create a scatter plot
scatter3D(x, y, z, phi = 0, bty = "g", pch = 20, cex = 0.5)
# Add text
text3D(x, y, z, labels = rownames(iris),
add = TRUE, colkey = FALSE, cex = 0.5)
# Line plots
# type ="l" for lines only
scatter3D(x, y, z, phi = 0, bty = "g", type = "l",
ticktype = "detailed", lwd = 4)

# type ="b" for both points and lines

scatter3D(x, y, z, phi = 0, bty = "g", type = "b",
ticktype = "detailed", pch = 20,
cex = c(0.5, 1, 1.5))

# type ="h" for vertical lines

scatter3D(x, y, z, phi = 0, bty = "g", type = "h",
ticktype = "detailed", pch = 19, cex = 0.5)

# Add confidence interval

# Confidence interval
CI <- list(z = matrix(nrow = length(x),
data = rep(0.1, 2*length(x))))
head(CI$z)

# 3D Scatter plot with CI

scatter3D(x, y, z, phi = 0, bty = "g", col = gg.col(100),
pch = 18, CI = CI)

# 3D fancy Scatter plot with small dots on basal plane

# A helper function scatter3D_fancy() is used:
# Add small dots on basal plane and on the depth plane
scatter3D_fancy <- function(x, y, z,..., colvar = z)
{
panelfirst <- function(pmat) {
XY <- trans3D(x, y, z = rep(min(z), length(z)), pmat = pmat)
scatter2D(XY$x, XY$y, colvar = colvar, pch = ".",
cex = 2, add = TRUE, colkey = FALSE)

XY <- trans3D(x = rep(min(x), length(x)), y, z, pmat = pmat)

scatter2D(XY$x, XY$y, colvar = colvar, pch = ".",
cex = 2, add = TRUE, colkey = FALSE)
}
scatter3D(x, y, z, ..., colvar = colvar, panel.first=panelfirst,
colkey = list(length = 0.5, width = 0.5, cex.clab = 0.75))
}

# Fancy scatter plot:

scatter3D_fancy(x, y, z, pch = 16,
ticktype = "detailed", theta = 15, d = 2,
main = "Iris data", clab = c("Petal", "Width (cm)") )

# Regression plane
# The mtcars data will be used:
data(mtcars)
head(mtcars[, 1:6])

# Use the function lm() to compute a linear regression model: ax + by + cz + d = 0

# Use the argument surf in scatter3D() function to add a regression surface.
# x, y, z variables
x <- mtcars$wt
y <- mtcars$disp
z <- mtcars$mpg
# Compute the linear regression (z = ax + by + d)
fit <- lm(z ~ x + y)
# predict values on regular xy grid
grid.lines = 26
x.pred <- seq(min(x), max(x), length.out = grid.lines)
y.pred <- seq(min(y), max(y), length.out = grid.lines)
xy <- expand.grid( x = x.pred, y = y.pred)
z.pred <- matrix(predict(fit, newdata = xy),
nrow = grid.lines, ncol = grid.lines)
# fitted points for droplines to surface
fitpoints <- predict(fit)
# scatter plot with regression plane
scatter3D(x, y, z, pch = 18, cex = 2,
theta = 20, phi = 20, ticktype = "detailed",
xlab = "wt", ylab = "disp", zlab = "mpg",
surf = list(x = x.pred, y = y.pred, z = z.pred,
facets = NA, fit = fitpoints), main = "mtcars")

# text3D: plot 3-dimensionnal texts

# The function text3D() is used as follow:
text3D(x, y, z, labels, ...)

# The USArrests data sets will be used in the example below:

data(USArrests)
with(USArrests, text3D(Murder, Assault, Rape,
labels = rownames(USArrests), colvar = UrbanPop,
col = gg.col(100), theta = 60, phi = 20,
xlab = "Murder", ylab = "Assault", zlab = "Rape",
main = "USA arrests", cex = 0.6,
bty = "g", ticktype = "detailed", d = 2,
clab = c("Urban","Pop"), adj = 0.5, font = 2))

# text3D and scatter3D

# Plot texts
with(USArrests, text3D(Murder, Assault, Rape,
labels = rownames(USArrests), colvar = UrbanPop,
col = gg.col(100), theta = 60, phi = 20,
xlab = "Murder", ylab = "Assault", zlab = "Rape",
 main = "USA arrests", cex = 0.6,
bty = "g", ticktype = "detailed", d = 2,
clab = c("Urban","Pop"), adj = 0.5, font = 2))
# Add points
with(USArrests, scatter3D(Murder, Assault, Rape - 1,
colvar = UrbanPop, col = gg.col(100),
type = "h", pch = ".", add = TRUE))

# Zoom near origin: choose suitable ranges

plotdev(xlim = c(0, 10), ylim = c(40, 150),
zlim = c(7, 25))

# display axis ranges

getplist()[c("xlim","ylim","zlim")]

# 3D Histogram
# The function hist3D() is used:
hist3D (x, y, z, ..., colvar = z,
col = NULL, add = FALSE)

# z: Matrix containing the values to be plotted

# x, y vectors with x and y values. x should be of length equal to nrow(z) and y should be equal to ncol(z)
# colvar: the variable used for coloring. If present, it should have the same dimension as z.
# col: color palette to be used for the colvar variable. By default a red-yellow-blue color scheme
(?jet.col) is used
# add: Logical. If TRUE, then the surfaces will be added to the current plot. If FALSE a new plot is started.
data(VADeaths)
# hist3D and ribbon3D with greyish background, rotated, rescaled,...
hist3D(z = VADeaths, scale = FALSE, expand = 0.01, bty = "g", phi = 20,
col = "#0072B2", border = "black", shade = 0.2, ltheta = 90,
space = 0.3, ticktype = "detailed", d = 2)

hist3D (x = 1:5, y = 1:4, z = VADeaths,

bty = "g", phi = 20, theta = -60,
xlab = "", ylab = "", zlab = "", main = "VADeaths",
col = "#0072B2", border = "black", shade = 0.8,
ticktype = "detailed", space = 0.15, d = 2, cex.axis = 1e-9)
# Use text3D to label x axis
text3D(x = 1:5, y = rep(0.5, 5), z = rep(3, 5),
labels = rownames(VADeaths),
add = TRUE, adj = 0)
# Use text3D to label y axis
text3D(x = rep(1, 4), y = 1:4, z = rep(0, 4),
labels = colnames(VADeaths),
add = TRUE, adj = 1)

# fancy 3D histograms
hist3D_fancy<- function(x, y, break.func = c("Sturges", "scott", "FD"), breaks = NULL,
 colvar = NULL, col="white", clab=NULL, phi = 5, theta = 25, ...){

# Compute the number of classes for a histogram

break.func <- break.func [1]
if(is.null(breaks)){
x.breaks <- switch(break.func,
Sturges = nclass.Sturges(x),
scott = nclass.scott(x),
FD = nclass.FD(x))
y.breaks <- switch(break.func,
Sturges = nclass.Sturges(y),
scott = nclass.scott(y),
FD = nclass.FD(y))
} else x.breaks <- y.breaks <- breaks

# Cut x and y variables in bins for counting

x.bin <- seq(min(x), max(x), length.out = x.breaks)
y.bin <- seq(min(y), max(y), length.out = y.breaks)
xy <- table(cut(x, x.bin), cut(y, y.bin))
z <- xy

xmid <- 0.5*(x.bin[-1] + x.bin[-length(x.bin)])

ymid <- 0.5*(y.bin[-1] + y.bin[-length(y.bin)])

oldmar <- par("mar")

par (mar = par("mar") + c(0, 0, 0, 2))
hist3D(x = xmid, y = ymid, z = xy, ...,
zlim = c(-max(z)/2, max(z)), zlab = "counts", bty= "g",
phi = phi, theta = theta,
shade = 0.2, col = col, border = "black",
d = 1, ticktype = "detailed")

scatter3D(x, y,
z = rep(-max(z)/2, length.out = length(x)),
colvar = colvar, col = gg.col(100),
add = TRUE, pch = 18, clab = clab,
colkey = list(length = 0.5, width = 0.5,
dist = 0.05, cex.axis = 0.8, cex.clab = 0.8)
)
par(mar = oldmar)
}

hist3D_fancy(quakes$long, quakes$lat, colvar=quakes$depth,

breaks =30)

hist3D_fancy(iris$Sepal.Length, iris$Petal.Width,
colvar=as.numeric(iris$Species))
# scatter2D: 2D scatter plot
# Create some data:
# x, y coordinates
set.seed(1234)
x <- sort(rnorm(10))
y <- runif(10)
# Variable for coloring points
col.v <- sqrt(x^2 + y^2)

# Basic 2D scatter plot:

scatter2D(x, y, colvar = col.v, pch = 16, bty ="n",
type ="b")

# type: plot types. Allowed values are:

# “b” to draw both points and line
# “h” for vertical line
# “l” for line only
# “p” for points only
# bty: box type

# 2D scatter plot with confidence interval:

# Confidence interval for x variable only
CI <- list()
CI$x <- matrix(nrow = length(x), data = c(rep(0.25, 2*length(x))))
scatter2D(x, y, colvar = col.v, pch = 16, bty ="n", cex = 1.5,
CI = CI, type = "b")

# Confidence interval for both x and y variables

CI$y <- matrix (nrow = length(y), data = c(rep(0.05, 2*length(y))))
CI$col <- "black"
scatter2D(x, y, colvar = col.v, pch = 16, bty ="n", cex = 1.5,
CI = CI, type ="b")

CI$y[c(2,4,8,10), ] <- NA # Some points have no CI

CI$x[c(2,4,8,10), ] <- NA # Some points have no CI
CI$alen <- 0.02 # increase arrow head
scatter2D(x, y, colvar = col.v, pch = 16, bty ="n", cex = 1.5,
CI = CI, type ="b")

# text2D
# Only text
with(USArrests, text2D(x = Murder, y = Assault + 5, colvar = Rape,
xlab = "Murder", ylab = "Assault", clab = "Rape",
main = "USA arrests", labels = rownames(USArrests), cex = 0.6,
adj = 0.5, font = 2))

# text with point

with(USArrests, text2D(x = Murder, y = Assault + 5, colvar = Rape,
xlab = "Murder", ylab = "Assault", clab = "Rape",
main = "USA arrests", labels = rownames(USArrests), cex = 0.6,
adj = 0.5, font = 2))
with(USArrests, scatter2D(x = Murder, y = Assault, colvar = Rape,
pch = 16, add = TRUE, colkey = FALSE))

# Other functions
# It’s also possible to draw arrows, segments and rectangles in a 3D or 2D plot using the functions
below:
arrows3D(x0, y0, z0, x1, y1, z1, ..., colvar = NULL,
col = NULL, type = "triangle", add = FALSE)
segments3D(x0, y0, z0, x1, y1, z1, ..., colvar = NULL,
col = NULL, add = "FALSE")
rect3D(x0, y0, y0, x1, y1, z1, ..., colvar = NULL,
col = NULL, add = FALSE)
arrows2D(x0, y0, z0, x1, y1, z1, ..., colvar = NULL,
col = NULL, type = "triangle", add = FALSE)
segments2D(x0, y0, z0, x1, y1, z1, ..., colvar = NULL,
col = NULL, add = "FALSE")
rect2D(x0, y0, y0, x1, y1, z1, ..., colvar = NULL,
col = NULL, add = FALSE)

# x0, y0, z0: coordinates of points from which to draw

# x1, y1, z1: coordinates of points to which to draw. For arrows3D and segments3D, at least one must be
supplied. For rect3D exactly one must be NULL.
# colvar: The variable used for coloring.
# col: color palette to be used for coloring. Default is red-yellow-blue color scheme.
# add: Logical. If TRUE, then the arrows, segments, … will be added to the current plot. If FALSE a new
plot is started.

# Prepare the data: we want to plot 4 arrows starting from the point of coordinates c(x0, y0, z0) and
ending at c(x1, y1, z1)
x0 <- c(0, 0, 0, 0)
y0 <- c(0, 0, 0, 0)
z0 <- c(0, 0, 0, 0)
x1 <- c(0.89, -0.46, 0.99, 0.96)
y1 <- c(0.36, 0.88, 0.02, 0.06)
z1 <- c(-0.28, 0.09, 0.05, 0.24)
cols <- c("#1B9E77", "#D95F02", "#7570B3", "#E7298A")

# 3D Arrows:
arrows3D(x0, y0, z0, x1, y1, z1, colvar = x1^2, col = cols,
lwd = 2, d = 3, clab = c("Quality", "score"),
main = "Arrows 3D", bty ="g", ticktype = "detailed")
# Add starting point of arrow
points3D(x0, y0, z0, add = TRUE, col="darkred",
colkey = FALSE, pch = 19, cex = 1)
# Add labels to the arrows
text3D(x1, y1, z1, c("Sepal.L", "Sepal.W", "Petal.L", "Petal.W"),
colvar = x1^2, col = cols, add=TRUE, colkey = FALSE)

# 2D arrows:
arrows2D(x0, y0, x1, y1, colvar = x1^2, col = cols,
lwd = 2, clab = c("Quality", "score"),
bty ="n", xlim = c(-1, 1), ylim = c(-1, 1))
# Add vertical and horizontal lines at c(0,0)
abline(h =0, v = 0, lty = 2)
# Add starting point of arrow
points2D(x0, y0, add = TRUE, col="darkred",
colkey = FALSE, pch = 19, cex = 1)
# Add labels to the arrows
text2D(x1, y1, c("Sepal.L", "Sepal.W", "Petal.L", "Petal.W"),
colvar = x1^2, col = cols, add=TRUE, colkey = FALSE)

# Note that, segments3D() and segments2D() are very similar to arrows3D() and arrows2D() and you can
play with them also.
# 3D rectangle: the R code below creates a rectangle with a transparent fill color (alpha = 0.5)
rect3D(x0 = 0, y0 = 0.5, z0 = 0, x1 = 1, z1 = 5,
ylim = c(0, 1), bty = "g", facets = TRUE,
border = "red", col ="#7570B3", alpha=0.5,
lwd = 2, phi = 20)

# 2D rectangle
rect2D(x0 = runif(3), y0 = runif(3),
x1 = runif(3), y1 = runif(3), colvar = 1:3,
alpha = 0.4, lwd = 2, main = "rect2D")

# Interactive plot
# To draw an interactive 3D plot the package plot3Drgl can be used.
#
# The package plot3Drgl allows to plot the graph generated with plot3D in openGL, as made available by
package rgl.
#
# The simplest way is to do as follow:
#
# Create base R-graphics using plot3D package
# Then use the function plotrgl() to draw the same figure in rgl
# Create his3D using plot3D
hist3D_fancy(iris$Sepal.Length, iris$Petal.Width, colvar=as.numeric(iris$Species))
# Make the rgl version
library("plot3Drgl")
plotrgl()
# Note that, after creating the rgl plot you can use the functions below:
#
# croprgl(xlim, ylim, zlim, …) to modify the ranges
# cutrgl(…) to zoom in on a selected region of the plot. The current plot will be overwritten
# uncutrgl(…) and uncroprgl(…) restore the original plot.
#
# …: any arguments for par3d, open3d or material3d in rgl package.