# Plots tracer distributions in 2-D. `tracers2D` plots a tracer distribution using traditional R graphics. The topography can be defined when calling this function. `tracers2Drgl` plots a tracer distribution in open-GL graphics. A suitable topography has to be created before calling this function. ```r tracers2D(x, y, colvar = NULL, ..., col = NULL, NAcol = "white", colkey = NULL, mask = NULL, image = FALSE, contour = FALSE, clim = NULL, clab = NULL) tracers2Drgl(x, y, colvar = NULL, ..., col = NULL, NAcol = "white", breaks = NULL, colkey = FALSE, clim = NULL, clab = NULL) ``` ## Arguments - `x, y`: Vectors with x- and y-coordinates of the tracers. Should be of equal length. - `colvar`: The variable used for coloring. It need not be present, but if specified, it should be a vector of dimension equal to `x`. Values of `NULL`, `NA`, or `FALSE` will toggle off coloration according to `colvar`. - `col`: Colors to be used for coloring each individual point (if colvar not specified) or that define the colors 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 from package `plot3D`. 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. - `contour, image`: If `TRUE`, then a contour2D or `image2D` plot will be added to the quiver plot. Also allowed is to pass a `list` with arguments for the contour2D or image2D function. - `clim`: Only if `colvar` is specified, the range of the colors, used for the color key. - `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. - `mask`: A `list` defining the grid cells outside the domain as `NA`. Use a list with argument `NAcol` to specify the color that the masked cells (that are `NA`) should get; the default is `"black"`. The unmasked cells are left `"white"`. `mask` should be a `list` that contains the `x`, `y`, and `z` values (and that are named 'x', 'y', 'z'). A `mask` cannot be combined with `add = TRUE`. - ``...``: additional arguments passed to the plotting method scatter2D . The arguments after `...` must be matched exactly. ## Returns returns nothing ## See Also tracers3D for plotting time series of tracer distributions in 3D Ltrans for the output of a particle tracking model ## Author(s) Karline Soetaert ## Examples ```r # save plotting parameters pm <- par("mfrow") ## ======================================================================= ## Create topography, data ## ======================================================================= # The topographic surface x <- seq(-pi, pi, by = 0.2) y <- seq(0, pi, by = 0.1) M <- mesh(x, y) z <- with(M, sin(x)*sin(y)) # Initial condition xi <- c(0.125 * rnorm(100) - pi/2, 0.125 * rnorm(100) - pi/4) yi <- 0.25 * rnorm(200) + pi/2 # the species species <- c(rep(1, 100), rep(2, 100)) # set initial conditions xp <- xi; yp <- yi ## ======================================================================= ## using a mask and contour ## ======================================================================= Z <- z; Z[abs(Z) < 0.1] <- NA par(mfrow = c(2, 2)) for (i in 1:4) { # update tracer distribution xp <- xp + 0.25 * rnorm(200) yp <- yp + 0.025 * rnorm(200) # plot new tracer distribution tracers2D(xp, yp, colvar = species, pch = ".", cex = 5, main = paste("timestep ", i), col = c("orange", "blue"), colkey = list(side = 1, length = 0.5, labels = c("sp1","sp2"), at = c(1.25, 1.75), dist = 0.075), NAcol = "black", mask = list(x = x, y = y, z = Z), contour = list(x = x, y = y, z = Z) ) } ## ======================================================================= ## using image and contour ## ======================================================================= for (i in 1:4) { # update tracer distribution xp <- xp + 0.25 * rnorm(200) yp <- yp + 0.025 * rnorm(200) # plot new tracer distribution tracers2D(xp, yp, colvar = species, pch = ".", cex = 5, main = paste("timestep ", i), col = c("orange", "blue"), colkey = list(side = 1, length = 0.5, labels = c("sp1","sp2"), at = c(1.25, 1.75), dist = 0.075), NAcol = "black", contour = list(x = x, y = y, z = z), image = list(x = x, y = y, z = z, colkey = TRUE)) } ## ======================================================================= ## rgl tracer plot ## ======================================================================= # here the image has to be drawn first image2Drgl(x = x, y = y, z = z) # set initial conditions xp <- xi; yp <- yi nstep <- 40 for (i in 1:nstep) { # update tracer distribution xp <- xp + 0.25 * rnorm(200) yp <- yp + 0.025 * rnorm(200) # plot new tracer distribution n tracers2Drgl(xp, yp, colvar = species, cex = 1, main = paste("timestep ", i), col = c("orange", "blue")) } # reset plotting parameters par(mfrow = pm) ```

tracers2D function