arrows3D: Plots arrows, segments, points, lines, polygons, rectangles... In plot3D: Plotting Multi-Dimensional Data

Description

Functions `arrows3D` and `segments3D` draw arrows and line segments between pairs of points.

Functions `box3D` and `border3D` draw boxes between pairs of points.

`polygon3D` draws polygons; `rect3D` draws rectangles.

The 2D functions `arrows2D`, `segments2D`, `rect2D` and `polygon2D` are included for their side effect of having a color key.

Usage

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62``` ```arrows3D (x0, y0, z0, x1 = x0, y1 = y0, z1 = z0, ..., colvar = NULL, phi = 40, theta = 40, col = NULL, NAcol = "white", breaks = NULL, colkey = NULL, panel.first = NULL, clim = NULL, clab = NULL, bty = "b", type = "triangle", add = FALSE, plot = TRUE) segments3D (x0, y0, z0, x1 = x0, y1 = y0, z1 = z0, ..., colvar = NULL, phi = 40, theta = 40, col = NULL, NAcol = "white", breaks = NULL, colkey = NULL, panel.first = NULL, clim = NULL, clab = NULL, bty = "b", add = FALSE, plot = TRUE) box3D (x0, y0, z0, x1, y1, z1, ..., colvar = NULL, phi = 40, theta = 40, col = NULL, NAcol = "white", breaks = NULL, border = NA, facets = TRUE, colkey = NULL, panel.first = NULL, clim = NULL, clab = NULL, bty = "b", add = FALSE, plot = TRUE) border3D(x0, y0, z0, x1, y1, z1, ..., colvar = NULL, phi = 40, theta = 40, col = NULL, NAcol = "white", breaks = NULL, colkey = NULL, panel.first = NULL, clim = NULL, clab = NULL, bty = "b", add = FALSE, plot = TRUE) rect3D (x0, y0, z0, x1 = NULL, y1 = NULL, z1 = NULL, ..., colvar = NULL, phi = 40, theta = 40, col = NULL, NAcol = "white", breaks = NULL, border = NA, facets = TRUE, colkey = NULL, panel.first = NULL, clim = NULL, clab = NULL, bty = "b", add = FALSE, plot = TRUE) polygon3D (x, y, z, ..., colvar = NULL, phi = 40, theta = 40, col = NULL, NAcol = "white", breaks = NULL, border = NA, facets = TRUE, colkey = NULL, panel.first = NULL, clim = NULL, clab = NULL, bty = "b", add = FALSE, plot = TRUE) arrows2D (x0, y0, x1 = x0, y1 = y0, ..., colvar = NULL, col = NULL, NAcol = "white", breaks = NULL, colkey = NULL, clim = NULL, clab = NULL, type = "triangle", add = FALSE, plot = TRUE) segments2D (x0, y0, x1 = x0, y1 = y0, ..., colvar = NULL, col = NULL, NAcol = "white", breaks = NULL, colkey = NULL, clim = NULL, clab = NULL, add = FALSE, plot = TRUE) rect2D (x0, y0, x1 = x0, y1 = y0, ..., colvar = NULL, col = NULL, NAcol = "white", breaks = NULL, colkey = NULL, clim = NULL, clab = NULL, add = FALSE, plot = TRUE) polygon2D (x, y, ..., colvar = NULL, col = NULL, NAcol = "white", breaks = NULL, border = NA, facets = TRUE, colkey = NULL, clim = NULL, clab = NULL, add = FALSE, plot = TRUE) ```

Arguments

 `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`. `x, y, z ` coordinates of the vertices of the polygon. The polygon will be closed by joining the last point to the first point. The coordinates can contain missing values (`NA`). These `NA` values break the polygon into several complete polygons. `colvar ` The variable used for coloring. It need not be present, but if specified, it should be a vector of dimension equal to the coordinates or to the number of polygons. Values of `NULL`, `NA`, or `FALSE` will toggle off coloration according to `colvar`. `theta, phi ` the angles defining the viewing direction. `theta` gives the azimuthal direction and `phi` the colatitude. See persp. `col ` Color palette to be used for coloring the arrows or segments as specified by the `colvar` variable. If `col` is `NULL` and `colvar` is specified, then a red-yellow-blue colorscheme (jet.col) will be used. If `col` is `NULL` and `colvar` is not specified, then `col` will be "black". `NAcol ` Colors to be used for `colvar` values that are `NA`. `breaks ` a set of finite numeric breakpoints for the colors; must have one more breakpoint than color and be in increasing order. Unsorted vectors will be sorted, with a warning. `colkey ` A logical, `NULL` (default), or a `list` with parameters for the color key (legend). List parameters should be one of ```side, plot, length, width, dist, shift, addlines, col.clab, cex.clab, side.clab, line.clab, adj.clab, font.clab``` and the axis parameters ```at, labels, tick, line, pos, outer, font, lty, lwd, lwd.ticks, col.box, col.axis, col.ticks, hadj, padj, cex.axis, mgp, tck, tcl, las```. The defaults for the parameters are ```side = 4, plot = TRUE, length = 1, width = 1, dist = 0, shift = 0, addlines = FALSE, col.clab = NULL, cex.clab = par("cex.lab"), side.clab = NULL, line.clab = NULL, adj.clab = NULL, font.clab = NULL```) See colkey. The default is to draw the color key on side = 4, i.e. in the right margin. If `colkey` = `NULL` then a color key will be added only if `col` is a vector. Setting `colkey = list(plot = FALSE)` will create room for the color key without drawing it. if `colkey = FALSE`, no color key legend will be added. `border ` The color of the lines drawn around the surface facets. The default, `NA`, will disable the drawing of borders. `facets ` If `TRUE`, then `col` denotes the color of the surface facets. If `FALSE`, then the surface facets are colored “white” and the `border` (if `NA`) will be colored as specified by `col`. If `NA` then the facets will be transparent. It is usually faster to draw with `facets = FALSE`. `panel.first ` A `function` to be evaluated after the plot axes are set up but before any plotting takes place. This can be useful e.g. for drawing background grids or scatterplot smooths. The function should have as argument the transformation matrix, e.g. it should be defined as `function(pmat)`. See example of persp3D and last example of voxel3D. `clab ` Only if `colkey` is not `NULL` or `FALSE`, the label to be written on top of the color key. The label will be written at the same level as the main title. To lower it, `clab` can be made a vector, with the first values empty strings. `clim ` Only if `colvar` is specified, the range of the color variable, used for the color key. Values of `colvar` that extend the range will be put to `NA`. `bty ` The type of the perspective box, the default draws only the back panels. Only effective if the persp argument (`box`) equals `TRUE` (this is the default). See perspbox. `type ` The type of the arrow head, one of `"simple"` (which uses R-function arrows), `"curved"` or `"triangle"` and `"cone"`. The latter two are the same in `plot3D` (but differ in package `plot3Drgl`). `add ` Logical. If `TRUE`, then the arrows, segments, ... will be added to the current plot. If `FALSE` a new plot is started. `plot ` Logical. If `TRUE` (default), a plot is created, otherwise the viewing transformation matrix is returned (as invisible). `...` additional arguments passed to the plotting methods. The following persp arguments can be specified: ```xlim, ylim, zlim, xlab, ylab, zlab, main, sub, r, d, scale, expand, box, axes, nticks, ticktype```. The arguments `xlim`, `ylim`, `zlim` only affect the axes for 3D plots. All objects will be plotted, including those that fall out of these ranges. To select objects only within the axis limits, use plotdev. `shade` and `lighting` arguments will have no effect. `alpha` can be given a value inbetween 0 and 1 to make colors transparent. In addition, the perspbox arguments `col.axis, col.panel, lwd.panel, col.grid, lwd.grid` can also be given a value. For `arrows3D`, the following arrows arguments can be specified: `length, code, angle`. For `polygon3D`, the following polygon arguments can be specified: `border`. For all the functions, arguments `lty, lwd` can be specified. The arguments after ... must be matched exactly.

Value

Returns the viewing transformation matrix.

See trans3D.

arrows for the 2-D arrows function on which `arrows3D` is based.
segments for the 2-D arrows function on which `segments3D` is based.
 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188``` ```# save plotting parameters pm <- par("mfrow") ## ======================================================================== ## arrows, points, segments, box ## ======================================================================== # Create a grid of x, y, and z values xx <- yy <- seq(-0.8, 0.8, by = 0.2) zz <- seq(-0.8, 0.8, by = 0.8) M <- mesh(xx, yy, zz) x0 <- M\$x; y0 <- M\$y; z0 <- M\$z x1 <- x0 + 0.1 Col <- c("red", "blue", "green") arrows3D(x0, y0, z0, x1 = x1, colvar = z0, lwd = 2, d = 2, clab = "z-value", col = Col, length = 0.1, xlim = c(-0.8, 0.8), ylim = c(-0.8, 0.8), main = "arrows3D, points3D, segments3D, border3D") # add starting point of arrows points3D(x0, y0, z0, add = TRUE, colvar = z0, colkey = FALSE, pch = ".", cex = 3, col = Col) # use segments to add section x0 <- c(-0.8, 0.8, 0.8, -0.8) x1 <- c( 0.8, 0.8, -0.8, -0.8) y0 <- c(-0.8, -0.8, 0.8, -0.8) y1 <- c(-0.8, 0.8, 0.8, 0.8) z0 <- c(0., 0., 0., 0.) segments3D(x0, y0, z0, x1, y1, z1 = z0, add = TRUE, col = "black", lwd = 2) # add a box border3D(-0.8, -0.8, -0.8, 0.8, 0.8, 0.8, col = "orange", add = TRUE, lwd = 3) ## ======================================================================== ## boxes, cubes ## ======================================================================== # borders are boxes without facets border3D(x0 = seq(-0.8, -0.1, by = 0.1), y0 = seq(-0.8, -0.1, by = 0.1), z0 = seq(-0.8, -0.1, by = 0.1), x1 = seq(0.8, 0.1, by = -0.1), y1 = seq(0.8, 0.1, by = -0.1), z1 = seq(0.8, 0.1, by = -0.1), col = gg.col(8), lty = 2, lwd = c(1, 4), phi = 20, main = "border3D") box3D(x0 = -0.8, y0 = -0.8, z0 = -0.8, x1 = 0.8, y1 = 0.8, z1 = 0.8, border = "black", lwd = 2, col = gg.col(1, alpha = 0.8), main = "box3D") box3D(x0 = seq(-0.8, -0.1, by = 0.1), y0 = seq(-0.8, -0.1, by = 0.1), z0 = seq(-0.8, -0.1, by = 0.1), x1 = seq(0.8, 0.1, by = -0.1), y1 = seq(0.8, 0.1, by = -0.1), z1 = seq(0.8, 0.1, by = -0.1), col = rainbow(n = 8, alpha = 0.1), border = "black", lwd = 2, phi = 20) # here the perspective does not always work # use alpha.col to set the transparency of a vector of colors box3D(x0 = runif(3), y0 = runif(3), z0 = runif(3), x1 = runif(3), y1 = runif(3), z1 = runif(3), col = c("red", "lightblue", "orange"), alpha = 0.5, border = "black", lwd = 2) ## ======================================================================== ## rectangles ## ======================================================================== # at constant 'z' rect3D(x0 = seq(-0.8, -0.1, by = 0.1), y0 = seq(-0.8, -0.1, by = 0.1), z0 = seq(-0.8, -0.1, by = 0.1), x1 = seq(0.8, 0.1, by = -0.1), y1 = seq(0.8, 0.1, by = -0.1), col = gg.col(8), border = "black", bty = "g", lwd = 2, phi = 20, main = "rect3D") # constant y and with transparent facets rect3D(x0 = 0, y0 = 0, z0 = 0, x1 = 1, z1 = 5, ylim = c(0, 1), facets = NA, border = "red", bty = "g", lwd = 2, phi = 20) # add rect at constant z, with colored facet rect3D(x0 = 0, y0 = 0, z0 = 0, x1 = 1, y1 = 1, border = "red", add = TRUE) ## ======================================================================== ## arrows added to a persp plot ## ======================================================================== x <- y <- seq(-10, 10, length = 30) z <- outer(x, y, FUN = function(x,y) x^2 + y^2) persp3D(x, y, z, theta = 30, phi = 30, col = "lightblue", ltheta = 120, shade = 0.75, ticktype = "detailed", xlab = "X", ylab = "Y", zlab = "x^2+y^2" ) # Points where to put the arrows x <- y <- seq(-10, 10, len = 6) X0 <- outer(x, y, FUN = function (x,y) x) Y0 <- outer(x, y, FUN = function (x,y) y) Z0 <- outer(x, y, FUN = function (x,y) x^2 + y^2) X1 <- X0 + 1 Y1 <- Y0 + 1 Z1 <- Z0 + 10 arrows3D(X0, Y0, Z0, X1, Y1, Z1, lwd = 2, add = TRUE, type = "curved", col = "red") segments3D(X0, Y0, Z0, X0, Y0, rep(0, length(X0)), lwd = 2, add = TRUE, col = "green") ## ======================================================================== ## polygon3D ## ======================================================================== x <- runif(10) y <- runif(10) z <- runif(10) polygon3D(x, y, z) # several polygons, separated by NAs x <- runif(39) y <- runif(39) z <- runif(39) ii <- seq(4, 36, by = 4) x[ii] <- y[ii] <- z[ii] <- NA # transparent colors (alpha) polygon3D(x, y, z, border = "black", lwd = 3, col = gg.col(length(ii) + 1, alpha = 0.8), main = "polygon3D") ## ======================================================================== ## 2D examples, with color key ## ======================================================================== arrows2D(x0 = runif(10), y0 = runif(10), x1 = runif(10), y1 = runif(10), colvar = 1:10, code = 3, main = "arrows2D, segments2D") segments2D(x0 = runif(10), y0 = runif(10), x1 = runif(10), y1 = runif(10), colvar = 1:10, lwd = 2, add = TRUE, colkey = FALSE) # transparency rect2D(x0 = runif(10), y0 = runif(10), x1 = runif(10), y1 = runif(10), colvar = 1:10, alpha = 0.4, lwd = 2, main = "rect2D") ## ======================================================================== ## polygon2D ## ======================================================================== x <- runif(10) y <- runif(10) polygon2D(x, y) # same as polygon # several polygons, separated by NAs x <- runif(59) y <- runif(59) ii <- seq(5, 55, by = 5) x[ii] <- y[ii] <- NA # transparent colors (alpha) polygon2D(x, y, border = "black", lwd = 3, colvar = 1:(length(ii) + 1), col = gg.col(), alpha = 0.2, main = "polygon2D") # restore plotting parameters par(mfrow = pm) ```