tracers3D plots 3D tracer distributions in traditional graphics.
The topography can be defined when calling this function or created before
calling this function.
tracers3Drgl plots 3D tracer distributions in open-GL graphics.
A suitable topography has to be created before calling this function.
It does not create a movie.
moviepoints3D creates a movie of tracer distributions
in open-GL graphics.
It is based on the plot3Drgl function points3Drgl.
Vectors with (x, y, z) positions of 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, y, z.
Values of NULL, NA, or FALSE
will toggle off coloration according to colvar.
t
Vectors with time points of tracers.
Should be of length equal to length of x, y ,z, colvar.
by
Number increment of the time sequence.
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.
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.
surf
If not NULL, a list specifying a surface to be added on
the scatterplot.
They should include at least x, y, z, equal sized
matrices, and optional: colvar, col, NAcol, border, facets,
lwd, resfac, clim, ltheta, lphi, shade, lighting. Note that the default is
that colvar is not specified.
add
Logical. If TRUE, then the points will be added to the current plot.
If FALSE a new plot is started.
ask
Logical. If TRUE, then new points will only be drawn after a key has been struck. If FALSE, redrawing will depend on wait
wait
The time interval inbetween drawing of a set of new points, in seconds.
If NULL, the drawing will not be suspended.
basename
The base name of a png file to be produced for each movieframe.
...
additional arguments passed to scatter3D from package
plot3D. Typical arguments are cex, main (both functions),
and pch, ... for tracers3D.
Value
returns nothing
Author(s)
Karline Soetaert <karline.soetaert@nioz.nl>
See Also
tracers2D for plotting time series of tracer distributions in 2D
movieslice3D for plotting slices in 3D
Ltrans for 3-D output of a particle tracking model
Examples
# 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(0.25 * rnorm(100) - pi/2, 0.25 * rnorm(100) - pi/4)
yi <- 0.25 * rnorm(200) + pi/2
zi <- 0.005*rnorm(200) + 0.5
# the species
species <- c(rep(1, 100), rep(2, 100))
# set initial conditions
xp <- xi; yp <- yi; zp <- zi
## =======================================================================
## Traditional graphics
## =======================================================================
par(mfrow = c(2, 2))
# Topography is defined by argument surf
for (i in 1:4) {
# update tracer distribution
xp <- xp + 0.25 * rnorm(200)
yp <- yp + 0.025 * rnorm(200)
zp <- zp + 0.25 *rnorm(200)
# plot new tracer distribution
tracers3D(xp, yp, zp, colvar = species, pch = ".", cex = 5,
main = paste("timestep ", i), col = c("orange", "blue"),
surf = list(x, y, z = z, theta = 0, facets = FALSE),
colkey = list(side = 1, length = 0.5, labels = c("sp1","sp2"),
at = c(1.25, 1.75), dist = 0.075))
}
# same, but creating topography first
## Not run:
# create the topography on which to add points
persp3D(x, y, z = z, theta = 0, facets = FALSE, plot = FALSE)
for (i in 1:4) {
# update tracer distribution
xp <- xp + 0.25 * rnorm(200)
yp <- yp + 0.025 * rnorm(200)
zp <- zp + 0.25 *rnorm(200)
# plot new tracer distribution
tracers3D(xp, yp, zp, 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))
}
## End(Not run)
## =======================================================================
## rgl graphics
## =======================================================================
# pause <- 0.05
# create a suitable topography
persp3D(x, y, z = z, theta = 0, facets = NA, plot = FALSE)
plotrgl( )
xp <- xi; yp <- yi; zp <- zi
nstep <- 10
for (i in 1:nstep) {
xp <- xp + 0.05 * rnorm(200) + 0.05
yp <- yp + 0.0025 * (rnorm(200) + 0.0025)
zp <- zp + 0.05 *rnorm(200)
# tracers3Drgl(xp, yp, zp, col = c(rep("orange", 100), rep("blue", 100)),
# main = paste("timestep ", i))
# or:
tracers3Drgl(xp, yp, zp, colvar = species, col = c("orange", "blue"),
main = paste("timestep ", i))
# Sys.sleep(pause)
# or: readline("hit enter for next")
}
# using function moviepoints3D
## Not run:
# first create the data in matrices
xp <- matrix(nrow = 200, ncol = nstep, data = xi)
yp <- matrix(nrow = 200, ncol = nstep, data = yi)
zp <- matrix(nrow = 200, ncol = nstep, data = zi)
tp <- matrix(nrow = 200, ncol = nstep, data = 0)
cv <- matrix(nrow = 200, ncol = nstep, data = species)
nstep <- 10
for (i in 2:nstep) {
xp[,i] <- xp[,i-1] + 0.05 * rnorm(200) + 0.05
yp[,i] <- yp[,i-1] + 0.0025 * (rnorm(200) + 0.0025)
zp[,i] <- zp[,i-1] + 0.05 *rnorm(200)
tp[,i] <- i
}
# create the topography
persp3Drgl(x, y, z = z, theta = 0, lighting = TRUE, smooth = TRUE)
# add moviepoints:
moviepoints3D (xp, yp, zp, colvar = cv, t = tp,
wait = 0.05, cex = 10, col = c("red", "orange"))
## End(Not run)
# reset plotting parameters
par(mfrow = pm)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(OceanView)
Loading required package: plot3D
Loading required package: plot3Drgl
Loading required package: rgl
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/OceanView/tracers3D.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Tracers in 3D
> ### Title: Plotting tracer distributions in 3D
> ### Aliases: tracers3D tracers3Drgl moviepoints3D
> ### Keywords: hplot
>
> ### ** Examples
>
> # 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(0.25 * rnorm(100) - pi/2, 0.25 * rnorm(100) - pi/4)
> yi <- 0.25 * rnorm(200) + pi/2
> zi <- 0.005*rnorm(200) + 0.5
>
> # the species
> species <- c(rep(1, 100), rep(2, 100))
>
> # set initial conditions
> xp <- xi; yp <- yi; zp <- zi
>
> ## =======================================================================
> ## Traditional graphics
> ## =======================================================================
>
> par(mfrow = c(2, 2))
>
> # Topography is defined by argument surf
> for (i in 1:4) {
+ # update tracer distribution
+ xp <- xp + 0.25 * rnorm(200)
+ yp <- yp + 0.025 * rnorm(200)
+ zp <- zp + 0.25 *rnorm(200)
+
+ # plot new tracer distribution
+ tracers3D(xp, yp, zp, colvar = species, pch = ".", cex = 5,
+ main = paste("timestep ", i), col = c("orange", "blue"),
+ surf = list(x, y, z = z, theta = 0, facets = FALSE),
+ colkey = list(side = 1, length = 0.5, labels = c("sp1","sp2"),
+ at = c(1.25, 1.75), dist = 0.075))
+ }
>
> # same, but creating topography first
> ## Not run:
> ##D # create the topography on which to add points
> ##D persp3D(x, y, z = z, theta = 0, facets = FALSE, plot = FALSE)
> ##D
> ##D for (i in 1:4) {
> ##D # update tracer distribution
> ##D xp <- xp + 0.25 * rnorm(200)
> ##D yp <- yp + 0.025 * rnorm(200)
> ##D zp <- zp + 0.25 *rnorm(200)
> ##D
> ##D # plot new tracer distribution
> ##D tracers3D(xp, yp, zp, colvar = species, pch = ".", cex = 5,
> ##D main = paste("timestep ", i), col = c("orange", "blue"),
> ##D colkey = list(side = 1, length = 0.5, labels = c("sp1","sp2"),
> ##D at = c(1.25, 1.75), dist = 0.075))
> ##D }
> ## End(Not run)
>
> ## =======================================================================
> ## rgl graphics
> ## =======================================================================
>
> # pause <- 0.05
> # create a suitable topography
> persp3D(x, y, z = z, theta = 0, facets = NA, plot = FALSE)
>
> plotrgl( )
> xp <- xi; yp <- yi; zp <- zi
>
> nstep <- 10
> for (i in 1:nstep) {
+ xp <- xp + 0.05 * rnorm(200) + 0.05
+ yp <- yp + 0.0025 * (rnorm(200) + 0.0025)
+ zp <- zp + 0.05 *rnorm(200)
+
+ # tracers3Drgl(xp, yp, zp, col = c(rep("orange", 100), rep("blue", 100)),
+ # main = paste("timestep ", i))
+ # or:
+ tracers3Drgl(xp, yp, zp, colvar = species, col = c("orange", "blue"),
+ main = paste("timestep ", i))
+ # Sys.sleep(pause)
+ # or: readline("hit enter for next")
+ }
>
> # using function moviepoints3D
>
> ## Not run:
> ##D # first create the data in matrices
> ##D xp <- matrix(nrow = 200, ncol = nstep, data = xi)
> ##D yp <- matrix(nrow = 200, ncol = nstep, data = yi)
> ##D zp <- matrix(nrow = 200, ncol = nstep, data = zi)
> ##D tp <- matrix(nrow = 200, ncol = nstep, data = 0)
> ##D cv <- matrix(nrow = 200, ncol = nstep, data = species)
> ##D nstep <- 10
> ##D for (i in 2:nstep) {
> ##D xp[,i] <- xp[,i-1] + 0.05 * rnorm(200) + 0.05
> ##D yp[,i] <- yp[,i-1] + 0.0025 * (rnorm(200) + 0.0025)
> ##D zp[,i] <- zp[,i-1] + 0.05 *rnorm(200)
> ##D tp[,i] <- i
> ##D }
> ##D # create the topography
> ##D persp3Drgl(x, y, z = z, theta = 0, lighting = TRUE, smooth = TRUE)
> ##D
> ##D # add moviepoints:
> ##D moviepoints3D (xp, yp, zp, colvar = cv, t = tp,
> ##D wait = 0.05, cex = 10, col = c("red", "orange"))
> ##D
> ## End(Not run)
>
> # reset plotting parameters
> par(mfrow = pm)
>
>
>
>
>
> dev.off()
null device
1
>