Impressive package for 3D and 4D graph - R software and data visualization - Easy Guides

Install plot3D package
Load plot3D package
Prepare the data
Scatter plots
- Functions for scatter plots and texts in 2D and 3D
- Basic scatter plot
- Change the type of the box around the plot
- Color palettes
- Change the color by groups
- Change the position of the legend
- 3D viewing direction
- Titles and axis labels
- Tick marks and labels
- Add points and text to an existing plot
Line plots
- Add confidence interval
- 3D fancy Scatter plot with small dots on basal plane
- Regression plane
text3D: plot 3-dimensionnal texts
text3D and scatter3D
3D Histogram
scatter2D: 2D scatter plot
text2D
Other functions
Interactive plot
Infos

In my previous articles, I already described how to make 3D graphs in R using the package below:

scatterplot3d, non interactive
scatter3d, interactive
rgl, interactive

To close the discussion about 3D, in this tutorial I’ll describe the impressive plot3D package and its extension plot3Drgl package.

plot3D, from Karline Soetaert, is an R package containing many functions for 2D and 3D plotting: scatter3D, points3D, lines3D,text3D, ribbon3d, hist3D, etc.

In addition to the x, y (and z) values, an additional data dimension can be represented by a color variable (argument colvar).

This “4D” plot (x, y, z, color) with a color legend is not (easily) possible using the packages mentioned above (scatterplot3d, scatter3d, rgl).

The package plot3Drgl allows to plot easily the graph generated with plot3D in openGL, as made available by package rgl. This is described at the end of the present article.

install.packages("plot3D")

library("plot3D")

We’ll use the iris data set in the following examples :

data(iris)head(iris)

 Sepal.Length Sepal.Width Petal.Length Petal.Width Species1 5.1 3.5 1.4 0.2 setosa2 4.9 3.0 1.4 0.2 setosa3 4.7 3.2 1.3 0.2 setosa4 4.6 3.1 1.5 0.2 setosa5 5.0 3.6 1.4 0.2 setosa6 5.4 3.9 1.7 0.4 setosa

# x, y and z coordinatesx <- sep.l <- iris$Sepal.Lengthy <- pet.l <- iris$Petal.Lengthz <- sep.w <- iris$Sepal.Width

iris data set gives the measurements of the variables sepal length and width and petal length and width, respectively, for 50 flowers from each of 3 species of iris. The species are Iris setosa, versicolor, and virginica.

Functions for scatter plots and texts in 2D and 3D

The function below will be used:

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)

x, y, z: vectors of point coordinates
colvar: a variable used for coloring
col: color palette used for coloring the colvar variable
labels: the text to be written
add: logical. If TRUE, then the points will be added to the current plot. If FALSE a new plot is started
…: additional persp arguments including xlim, ylim, zlim, xlab, ylab, zlab, main, sub, r, d, scale, expand, box, axes, nticks, tictype.

Note that:

points3D and lines3D are shorthand for scatter3D(…, type =“p”) and scatter3D(…, type = “l”), respectively.
points2D and lines2D are shorthand for scatter2D(…, type = “p”) and scatter2D(…, type =“l”), respectively.

Basic scatter plot

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

The argument clab is used to change the title of the color legend.

By default, the points are colored automatically using the variable Z

In the R code below:

colvar = NULL: avoids coloring by z variable
col = “blue”: changes point colors to blue
pch = 19: changes point shapes
cex = 0.5: changes the size of points

scatter3D(x, y, z, colvar = NULL, col = "blue", pch = 19, cex = 0.5)

Change the type of the box around the plot

The argument bty is used. Allowed values are:

“f”: full box
“b”: default value. Only the back panels are visible
“b2”: back panels and grid lines are visible
“g”: grey background with white grid lines
“bl”: black background
“bl2”: black background with grey lines
“u”: means that the user will specify the arguments col.axis, col.panel, lwd.panel, col.grid, lwd.grid manually
“n”: no box will be drawn. This is the same as setting box = FALSE

# full boxscatter3D(x, y, z, bty = "f", colkey = FALSE, main ="bty= 'f'")# back panels and grid lines are visiblescatter3D(x, y, z, bty = "b2", colkey = FALSE, main ="bty= 'b2'" )

# grey background with white grid linesscatter3D(x, y, z, bty = "g", colkey = FALSE, main ="bty= 'g'")# User definedscatter3D(x, y, z, pch = 18, bty = "u", colkey = FALSE, main ="bty= 'u'", col.panel ="steelblue", expand =0.4, col.grid = "darkblue")

The argument colkey = FALSE is used to remove the legend.

Color palettes

Several color palettes are available in plot3D package:

jet.col(n, alpha): generates the matlab-type colors. This is the default color palette used in plot3D
jet2.col(n, alpha): similar to jet.col() but lacks the deep blue colors
gg.col(n, alpha) and gg2.col(n, alpha) generates gg-plot-like colors
ramp.col(col = c(“grey”, “black”), n, alpha): creates color schemes by interpolation
alpha.col(col = “grey”, alpha): creates transparent colors

n: Number of colors to generate. Default value is 100
alpha: color transparency. Value in the range 0, 1. Default value is 1
col: Colors to interpolate

# gg.col: ggplot2 like colorscatter3D(x, y, z, bty = "g", pch = 18, col = gg.col(100))# ramp.col: custom palettesscatter3D(x, y, z, bty = "g", pch = 18, col = ramp.col(c("blue", "yellow", "red")) )

Change the color by groups

The colkey is customized (see ?colkey for more details):

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 colkeyscatter3D(x, y, z, bty = "g", colkey = list(side = 1, length = 0.5))

The argument side is used to specify the colkey position: 1: for bottom, 2: for left, 3: for top, 4: for right.

3D viewing direction

The arguments theta and phi can be used to define the angles for the viewing direction. theta is the azimuthal direction and phi the co-latitude.

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

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

The default values for theta and phi are 40.

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

The arguments below can be used:

ticktype: Possible values are

“simple” draws just an arrow parallel to the axis to indicate direction of increase
“detailed” draws normal ticks and labels

nticks: the number of tick marks to draw on the axes. It has no effect if ticktype =“simple”.

 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 texttext3D(x, y, z, labels = rownames(iris), add = TRUE, colkey = FALSE, cex = 0.5)

# 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 linesscatter3D(x, y, z, phi = 0, bty = "g", type = "h", ticktype = "detailed", pch = 19, cex = 0.5)

Vertical lines are useful to see clearly the x-y location of points.

Add confidence interval

The argument CI is used. It’s a list containing the parameters and values for the confidence intervals or NULL.

If CI is a list, it should contain at least the item x, y or z (latter for scatter3D).These should be 2-columned matrices, defining the left/right intervals.

Other parameters should be one of: alen = 0.01, lty = par(“lty”), lwd = par(“lwd”), col = NULL, to set the length of the arrow head, the line type and width, and the color.

If col is NULL, then the colors as specified by colvar are used.

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

 [,1] [,2][1,] 0.1 0.1[2,] 0.1 0.1[3,] 0.1 0.1[4,] 0.1 0.1[5,] 0.1 0.1[6,] 0.1 0.1

# 3D Scatter plot with CIscatter3D(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 planescatter3D_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])

 mpg cyl disp hp drat wtMazda RX4 21.0 6 160 110 3.90 2.620Mazda RX4 Wag 21.0 6 160 110 3.90 2.875Datsun 710 22.8 4 108 93 3.85 2.320Hornet 4 Drive 21.4 6 258 110 3.08 3.215Hornet Sportabout 18.7 8 360 175 3.15 3.440Valiant 18.1 6 225 105 2.76 3.460

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 variablesx <- mtcars$wty <- mtcars$dispz <- mtcars$mpg# Compute the linear regression (z = ax + by + d)fit <- lm(z ~ x + y)# predict values on regular xy gridgrid.lines = 26x.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 surfacefitpoints <- predict(fit)# scatter plot with regression planescatter3D(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")

surf is a list specifying a (fitted) surface to be added on the scatter plot. The list should include at least x, y, z, defining the surface.

Other optional parameters can be specified in the surf argument including: colvar, col, NAcol, border, facets, lwd, resfac, clim, ltheta, lphi, shade, lighting, fit. (see ?surf3D for more details on these parameters)

Note that, by default colvar = z.
The argument fit should give the fitted z-values, in the same order as the z-values of the scatter points, for instance produced by predict(). When present, this will produce droplines from points to the fitted surface.

Note that, the function expand.grid(), in the R code above, creates a data frame from all combinations of factors

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))

# Plot textswith(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))

Note that, in order to choose suitable ranges for zooming, you can display axis ranges as follow:

# display axis ranges getplist()[c("xlim","ylim","zlim")]

$xlim[1] 0.8 17.4$ylim[1] 45 337$zlim[1] 7.3 46.0

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))

Create some data:

# x, y coordinatesset.seed(1234)x <- sort(rnorm(10)) y <- runif(10)# Variable for coloring pointscol.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 onlyCI <- 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 variablesCI$y <- matrix (nrow = length(y), data = c(rep(0.05, 2*length(y))))CI$col <- "black"scatter2D(x, y, colvar = col.v, pch = 16, bty ="n", cex = 1.5, CI = CI, type ="b")

CI$y[c(2,4,8,10), ] <- NA # Some points have no CICI$x[c(2,4,8,10), ] <- NA # Some points have no CICI$alen <- 0.02 # increase arrow headscatter2D(x, y, colvar = col.v, pch = 16, bty ="n", cex = 1.5, CI = CI, type ="b")

# Only textwith(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))

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 arrowpoints3D(x0, y0, z0, add = TRUE, col="darkred", colkey = FALSE, pch = 19, cex = 1)# Add labels to the arrowstext3D(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 arrowpoints2D(x0, y0, add = TRUE, col="darkred", colkey = FALSE, pch = 19, cex = 1)# Add labels to the arrowstext2D(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)

In the R code above, facets = FALSE, will remove the rectangle fill color.

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")

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

The package rgl allows to interactively rotate, zoom the graphs. However it’s not yet possible to plot a colorkey

# Create his3D using plot3Dhist3D_fancy(iris$Sepal.Length, iris$Petal.Width, colvar=as.numeric(iris$Species))# Make the rgl versionlibrary("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.

This analysis has been performed using R software (ver. 3.1.2) and plot3D (ver. 1.0-2)

References:

Karline Soetaert. plot3D: Tools for plotting 3-D and 2-D data. http://cran.r-project.org/web/packages/plot3D/vignettes/plot3D.pdf

Impressive package for 3D and 4D graph - R software and data visualization - Easy Guides - Wiki (2024)