| Title: | Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams |
|---|---|
| Description: | Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualising webs, electrical networks, etc. Support for the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter M.J. Herman (2009), Springer. and the book "Solving Differential Equations in R" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012), Springer. Includes demo(flowchart), demo(plotmat), demo(plotweb). |
| Authors: | Karline Soetaert <[email protected]> |
| Maintainer: | Karline Soetaert <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.6.5 |
| Built: | 2024-12-21 06:28:33 UTC |
| Source: | CRAN |
Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualising webs,...
Support for the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter M.J. Herman (2009). Springer.
and for the book "Solving Differential Equations in R" by Karline Soetaert, Jeff R. Cash and Francesca Mazzia (in press). Springer.
| Package: | diagram |
| Type: | Package |
| Version: | 1.6 |
| Date: | 2011-06-01 |
| License: | GNU Public License 2 or above |
This package is used in R-package ecolMod, which includes many more examples.
Karline Soetaert (Maintainer)
plotmat, plotweb, coordinates,
openplotmat,
arrows:
bentarrow,
curvedarrow, segmentarrow,
selfarrow, splitarrow,
straightarrow, treearrow,
boxes and text:
shadowbox, textdiamond,
textellipse, textempty, texthexa,
textdiamond, textplain, textrect,
textround.
electrical networks:
en.Resistor,en.Capacitator,en.Node,
en.Amplifier,en.Signal en.Ground.
## Not run: ## show examples (see respective help pages for details) example(plotmat) example(plotweb) ## run demos demo("flowchart") # creating flow charts demo("plotmat") # plotting diagrams inputted as a matrix demo("plotweb") # plotting webs inputted as a matrix ## open the directory with source code of demos browseURL(paste(system.file(package="diagram"), "/demo", sep="")) ## show package vignette vignette("diagram") edit(vignette("diagram")) browseURL(paste(system.file(package="diagram"), "/doc", sep="")) ## End(Not run)## Not run: ## show examples (see respective help pages for details) example(plotmat) example(plotweb) ## run demos demo("flowchart") # creating flow charts demo("plotmat") # plotting diagrams inputted as a matrix demo("plotweb") # plotting webs inputted as a matrix ## open the directory with source code of demos browseURL(paste(system.file(package="diagram"), "/demo", sep="")) ## show package vignette vignette("diagram") edit(vignette("diagram")) browseURL(paste(system.file(package="diagram"), "/doc", sep="")) ## End(Not run)
Connects two points with 2 segments (default = horizontal-vertical) and adds an arrowhead on (one of) the segments and at a certain distance.
bentarrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, arr.side = 2, arr.pos = 0.5, path = "H", ...)bentarrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, arr.side = 2, arr.pos = 0.5, path = "H", ...)
from |
coordinates (x,y) of the point *from* which to draw arrow. |
to |
coordinates (x,y) of the point *to* which to draw arrow. |
lwd |
line width. |
lty |
line type. |
lcol |
line color. |
arr.col |
arrowhead color. |
arr.side |
segment number on which arrowhead is drawn (1,2). |
arr.pos |
relative position of arrowhead on segment on which arrowhead is drawn. |
path |
first segment to be drawn (V=Vertical, H=Horizontal). |
... |
other arguments passed to function straightarrow. |
a two-segmented arrow is drawn between two points '(from, to)'
how the segments are drawn is set with path which can take on
the values:
H: (horizontal): first left or right, then vertical.
V: (vertical) : first down- or upward, then horizontal.
The segment(s) on which the arrow head is drawn is set with arr.side,
which is one or more values in (1, 2)
The position of the arrowhead on the segment on which it is drawn,
is set with arr.pos, a value between 0(start of segment) and 1
(end of segment).
The type of the arrowhead is set with arr.type which can take the
values:
"none" : skips the drawing of arrows.
"simple" : uses comparable R function arrows.
"triangle": uses filled triangle.
"curved" : draws arrowhead with curved edges.
"circle" : draws circular head.
"ellipse" : draws ellepsoid head.
"T" : draws T-shaped (blunt) head.
The size of the arrow head can be specified with the arguments
arr.length and arr.width.
See Arrowhead from package shape for details on
arrow head.
coordinates (x,y) where arrowhead is drawn
Karline Soetaert <[email protected]>
straightarrow, segmentarrow,
curvedarrow,
selfarrow, treearrow, splitarrow,
arrows: the comparable R function,
Arrows: more complicated arrow function from package
shape.
openplotmat(main = "bentarrow") pos <- cbind( A <- seq(0.1, 0.9, by = 0.2), rev(A)) text(pos, LETTERS[1:5], cex = 2) for (i in 1:4) bentarrow(from = pos[i,] + c(0.05, 0), to = pos[i+1,] + c(0, 0.05), arr.pos = 1, arr.adj = 1) for (i in 1:2) bentarrow(from = pos[i,] + c(0.05, 0), to = pos[i+1, ] + c(0, 0.05), arr.pos = 0.5, path = "V", lcol = "lightblue", arr.type = "triangle") bentarrow(from = pos[3, ] + c(0.05, 0), to = pos[4, ] + c(0, 0.05), arr.pos = 0.7, arr.side = 1, path = "V", lcol = "darkblue") bentarrow(from = pos[4, ] + c(0.05, 0), to = pos[5, ] + c(0, 0.05), arr.pos = 0.7, arr.side = 1:2, path = "V", lcol = "blue")openplotmat(main = "bentarrow") pos <- cbind( A <- seq(0.1, 0.9, by = 0.2), rev(A)) text(pos, LETTERS[1:5], cex = 2) for (i in 1:4) bentarrow(from = pos[i,] + c(0.05, 0), to = pos[i+1,] + c(0, 0.05), arr.pos = 1, arr.adj = 1) for (i in 1:2) bentarrow(from = pos[i,] + c(0.05, 0), to = pos[i+1, ] + c(0, 0.05), arr.pos = 0.5, path = "V", lcol = "lightblue", arr.type = "triangle") bentarrow(from = pos[3, ] + c(0.05, 0), to = pos[4, ] + c(0, 0.05), arr.pos = 0.7, arr.side = 1, path = "V", lcol = "darkblue") bentarrow(from = pos[4, ] + c(0.05, 0), to = pos[5, ] + c(0, 0.05), arr.pos = 0.7, arr.side = 1:2, path = "V", lcol = "blue")
estimates coordinates of elements, neatly arranged on a plot.
coordinates(pos = NULL, mx = 0.0, my = 0.0, N = length(pos), hor = TRUE, relsize = 1)coordinates(pos = NULL, mx = 0.0, my = 0.0, N = length(pos), hor = TRUE, relsize = 1)
pos |
vector specifying the number of elements in each row, or
2-columned matrix with element position, or |
mx |
horizontal shift (x). |
my |
vertical shift (y). |
N |
total number of elements to be positioned - only if pos= |
hor |
only if |
relsize |
scaling factor as a function of graph size. |
the position of the elements are specified with pos, which is
either NULL, or a vector specifying the number of elements on a row,
or a 2-columned matrix specifying the (x,y) position of each element.
when pos is NULL, the elements will be arranged
on a circle; in this case, the number of elements to be
positioned must be specified with N.
when pos is a vector, it specifies the number of elements
in each row (if hor =TRUE) or in each column (if
hor = FALSE).
For instance, with hor=TRUE and pos = c(3,2,1) the
elements will be arranged in 3 rows (length of vector); on the top row
3 elements; on the second row 2; and on the third row 1
element will be positioned. All elements within a row are equally
distributed horizontally; all rows are equally distributed vertically;
when pos is a matrix, it specifies the x(1st column) and
y(2nd column) position of each element and is returned as such.
The offset from the x-axis and from the y-axis can be changed with
mx and my.
2-columned matrix, with coordinates (x,y) of each of the elements
Karline Soetaert <[email protected]>
openplotmat(main = "coordinates") text(coordinates(N = 6), lab = LETTERS[1:6], cex = 2) text(coordinates(N = 8, relsize = 0.5), lab = letters[1:8], cex = 2) openplotmat(main = "coordinates") text(coordinates(pos = c(2, 4, 2)), lab = letters[1:8], cex = 2) plot(0, type = "n", xlim = c(0, 5), ylim = c(2, 8), main = "coordinates") text(coordinates(pos = c(2, 4, 3), hor = FALSE), lab = 1:9, cex = 2)openplotmat(main = "coordinates") text(coordinates(N = 6), lab = LETTERS[1:6], cex = 2) text(coordinates(N = 8, relsize = 0.5), lab = letters[1:8], cex = 2) openplotmat(main = "coordinates") text(coordinates(pos = c(2, 4, 2)), lab = letters[1:8], cex = 2) plot(0, type = "n", xlim = c(0, 5), ylim = c(2, 8), main = "coordinates") text(coordinates(pos = c(2, 4, 3), hor = FALSE), lab = 1:9, cex = 2)
Connects two points with an ellipsoid line and adds an arrowhead at a certain distance
curvedarrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, arr.pos = 0.5, curve = 1, dr = 0.01, endhead = FALSE, segment = c(0, 1), ...)curvedarrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, arr.pos = 0.5, curve = 1, dr = 0.01, endhead = FALSE, segment = c(0, 1), ...)
from |
coordinates (x,y) of the point *from* which to draw arrow. |
to |
coordinates (x,y) of the point *to* which to draw arrow. |
lwd |
line width. |
lty |
line type. |
lcol |
line color. |
arr.col |
arrowhead color. |
arr.pos |
relative position of arrowhead. |
curve |
relative size of curve (fraction of points distance) - see details. |
dr |
size of segments, in radians, to draw ellipse (decrease for smoother). |
endhead |
if |
segment |
if not |
... |
arguments passed to function |
A curved arrow is drawn between two points '(from, to)'
The position of the arrowhead, is set with arr.pos, a value between
0(start point) and 1(endpoint)
The line curvature is set with curve which expresses the ellipse
radius as a fraction of the distance between the two points.
For instance, curve=0.5 will draw an ellepse with small radius
half of a circle.
The type of the arrowhead is set with arr.type which can take
the values:
"none" : skips the drawing of arrows.
"simple" : uses comparable R function arrows.
"triangle": uses filled triangle.
"curved" : draws arrowhead with curved edges.
"circle" : draws circular head.
"ellipse" : draws ellepsoid head.
"T" : draws T-shaped (blunt) head.
The size of the arrow head can be specified with the arguments
arr.length and arr.width.
See Arrowhead from package shape for details on
arrow head
default |
coordinates (x,y) where arrowhead is drawn. |
Karline Soetaert <[email protected]>
straightarrow, segmentarrow,
bentarrow,
selfarrow, treearrow, splitarrow,
arrows: the comparable R function,
Arrows: more complicated arrow function from package
shape.
openplotmat(main = "curvedarrow") pos <- coordinates(pos = 4, my = 0.2) text(pos, LETTERS[1:4], cex = 2) for (i in 1:3) curvedarrow(from = pos[1, ] + c(0,-0.05), to = pos[i+1, ] + c(0,-0.05), curve = 0.5, arr.pos = 1) for (i in 1:3) curvedarrow(from = pos[1, ] + c(0, 0.05), to = pos[i+1, ] + c(0, 0.05), curve = -0.25, arr.adj = 1, arr.pos = 0.5, arr.type = "triangle", arr.col = "blue")openplotmat(main = "curvedarrow") pos <- coordinates(pos = 4, my = 0.2) text(pos, LETTERS[1:4], cex = 2) for (i in 1:3) curvedarrow(from = pos[1, ] + c(0,-0.05), to = pos[i+1, ] + c(0,-0.05), curve = 0.5, arr.pos = 1) for (i in 1:3) curvedarrow(from = pos[1, ] + c(0, 0.05), to = pos[i+1, ] + c(0, 0.05), curve = -0.25, arr.adj = 1, arr.pos = 0.5, arr.type = "triangle", arr.col = "blue")
Adds a resistor, capacitator, node, amplifier, ... to a diagrom
en.Resistor (mid, width = 0.05, length = 0.1, lab = NULL, pos = 0, dtext = 0., vert = TRUE, ...) en.Capacitator (mid, width = 0.025, length = 0.1, lab = NULL, pos = 2.5, dtext = 0.04, vert = TRUE, ...) en.Transistor (mid, gate, drain, source, r = 0.05, lab = NULL, pos = 0, dtext = 0, ...) en.Node(mid, cex = 1, lab = NULL, pos = 2.5, dtext = 0.025, ...) en.Amplifier(mid, r = 0.05, lab = NULL, pos = 0, dtext = 0, ...) en.Signal(mid, r = 0.03, lab = NULL, pos = 0, dtext = 0.025, ...) en.Ground(mid, width = 0.075, length = 0.1, n = 4, dx = 0.2, ...) enResistor(...)en.Resistor (mid, width = 0.05, length = 0.1, lab = NULL, pos = 0, dtext = 0., vert = TRUE, ...) en.Capacitator (mid, width = 0.025, length = 0.1, lab = NULL, pos = 2.5, dtext = 0.04, vert = TRUE, ...) en.Transistor (mid, gate, drain, source, r = 0.05, lab = NULL, pos = 0, dtext = 0, ...) en.Node(mid, cex = 1, lab = NULL, pos = 2.5, dtext = 0.025, ...) en.Amplifier(mid, r = 0.05, lab = NULL, pos = 0, dtext = 0, ...) en.Signal(mid, r = 0.03, lab = NULL, pos = 0, dtext = 0.025, ...) en.Ground(mid, width = 0.075, length = 0.1, n = 4, dx = 0.2, ...) enResistor(...)
mid |
midpoint (x,y) of the symbol. |
width |
width of the symbol. |
length |
length of the symbol. |
lab |
one label to be added in the symbol. |
pos |
position of the label in the symbol; 1 = below; 2 = left; 3 = upper, 4 = right; 1.5 = below-left, ... |
dtext |
shift in x- and/or y-direction for the text |
vert |
if |
gate |
position (x,y) of the gate terminal of the |
drain |
position (x,y) of the drain terminal of the |
source |
position (x,y) of the source terminal of the |
r |
radius of |
cex |
size of node pch ( |
n |
number of horizontal lines in ( |
dx |
size reduction of horizontal lines in ( |
... |
other arguments passed to functions. |
Created for drawing the electrical network in the book Soetaert Karline, Jeff Cash and Francesca Mazzia. Solving differential equations in R. Springer.
enResistor is synonymous for en.Resistor (to trick the builder in adding this help file to the package)
Karline Soetaert <[email protected]>.
textdiamond, textellipse, textempty,
texthexa, textmulti, textplain,
textround
## ============================================================================= ## en.Capacitator ## ============================================================================= emptyplot(main = "en.Capacitator") straightarrow(c(0.5, 0.9), c(0.5, 0.1), arr.pos = 0.3, arr.length = 0.25, arr.type = "triangle") en.Capacitator(c(0.5, 0.5), width = 0.075, length = 0.5, vert = TRUE) text(0.4, 0.65, "i", font = 3, cex = 2) straightarrow(c(0.8, 0.3), c(0.8, 0.77), arr.pos = 1, arr.length = 0.25, arr.type = "triangle", lwd = 1) text(0.925, 0.65, "v", font = 3, cex = 2) text(0.15, 0.5, "C", font = 3, cex = 2) box(col = "grey") ## ============================================================================= ## en.Resistor ## ============================================================================= emptyplot(main = "en.Resistor") straightarrow(c(0.5, 0.9), c(0.5, 0.1), arr.pos = 0.2, arr.length = 0.25, arr.type = "triangle", lwd = 1) text(0.4, 0.85, "i", font = 3, cex = 2) en.Resistor(c(0.5, 0.5), width = 0.25, length = 0.35 ) straightarrow(c(0.8, 0.3), c(0.8, 0.77), arr.pos = 1, arr.length = 0.25, arr.type = "triangle", lwd = 1) text(0.925, 0.65, "v", font = 3, cex = 2) text(0.5, 0.5, "R", font = 3, cex = 2) box(col = "grey") ## ============================================================================= ## en.Signal ## ============================================================================= emptyplot(main = "voltage source, en.Signal") lines(c(0.5, 0.5), c(0.1, 0.9)) en.Signal(c(0.5, 0.5), r = 0.15) straightarrow(c(0.8, 0.3), c(0.8, 0.77), arr.pos = 1, arr.length = 0.25, arr.type = "triangle", lwd = 1) text(0.925, 0.65, "v", font = 3, cex = 2) box(col = "grey") ## ============================================================================= ## en.Ground ## ============================================================================= emptyplot(main = "en.Ground") straightarrow(c(0.5, 0.7), c(0.5, 0.25), arr.pos = 1.0, arr.length = 0.25, arr.type = "triangle", lwd = 1) en.Ground(c(0.5, 0.65), width = 0.25, length = 0.35 ) box(col = "grey") ## ============================================================================= ## en.Node ## ============================================================================= emptyplot(main = "en.Node") rect(0.2, 0.2, 0.8, 0.8) en.Node(c(0.2, 0.2), lab = "N1" , pos = 1.5) en.Node(c(0.2, 0.8), lab = "N2" , pos = 2.5) en.Node(c(0.8, 0.8), lab = "N3" , pos = 3.5) en.Node(c(0.8, 0.2), lab = "N2" , pos = 4.5) box(col = "grey") ## ============================================================================= ## en.Amplifier example ## ============================================================================= emptyplot(main = "en.Amplifier") en.Amplifier(c(0.5, 0.5), r = 0.15) box(col = "grey") ## ============================================================================= ## en.Transistor example ## ============================================================================= emptyplot(main = "enTransistor") gate <- c(0.1, 0.5) mid <- c(0.5, 0.5) drain <- c(0.9, 0.9) source <- c(0.9, 0.1) en.Transistor(mid = mid, gate = gate, drain = drain, source = source, r = 0.15) text(0.2, 0.4, "Gate", font = 3) text(0.8, 0.9, "Drain", font = 3, adj = 1) text(0.8, 0.1, "Source", font = 3, adj = 1) box(col = "grey") ## ============================================================================= ## position of text examples ## ============================================================================= mf <- par (mfrow = c(2, 2)) openplotmat(main = "pos") segments(0, 0.5, 1, 0.5) for (i in 4:0) en.Resistor( mid = c(0.5, 0.5), width = 0.25, length = 0.25, lab = i, pos = i, dtext = 0.2) openplotmat(main = "pos") segments(0, 0.5, 1, 0.5) for (i in 1:4) en.Resistor( mid = c(0.5, 0.5), width = 0.25, length = 0.25, lab = i+0.5, pos = i+0.5, dtext = 0.25) openplotmat(main = "vert = TRUE") segments(0.5, 0, 0.5, 1) for (i in 1:4) en.Resistor( mid = c(0.5, i/5), width = 0.075, length = 0.125, lab = substitute(R[i], list(i = i) )) openplotmat(main = "vert = FALSE") segments(0, 0.5, 1, 0.5) for (i in 1:4) en.Resistor( mid = c(i/5, 0.5), width = 0.075, length = 0.125, lab = substitute(R[i], list(i = i) ), vert = FALSE) par(mfrow = mf) ## ============================================================================= ## A small transistor example ## ============================================================================= par(lwd = 1.5) par(mar = c(0, 0, 2, 0)) emptyplot(main = "transistor Amplifier", ylim = c(-0.1, 1), xlim = c(-0.1, 1.1), asp = FALSE) x1 <- 0; x2 <- 0.2; x3 <- 0.4; x4 <- 0.6; x5 <- 0.8; x6 <- 1; y1 <- 0.05; y2 <- 0.4; y3 <- 0.5; y4 <- 0.6; y5 <- 0.95 x23 <- (x2 + x3)/2 x56 <- (x5 + x6)/2 lines(c(x2, x6, x6, x2, x2, x1, x1, x23, x3, x3), c(y1, y1, y5, y5, y1, y1, y3, y3, y4, y5)) lines(c(x3, x3), c(y2, y1)) lines(c(x3, x4, x4), c(y2, y2, y1)) lines(c(x3, x5, x5), c(y4, y4, y1)) en.Transistor(mid = c(x23, y3), gate = c(x2, y3), drain = c(x3,y4), source = c(x3,y2), r = 0.035) en.Signal(c(x1, 0.2), lab = expression("U"["in"])) en.Signal(c(x6, y2), lab = expression("U"["b"])) straightarrow(c(x1 - 0.05, 0.23), c(x1 - 0.05, 0.17), arr.pos =1, arr.type = "triangle", lwd = 1) straightarrow(c(x6 + 0.05, y2 + 0.03), c(x6 + 0.05, y2 - 0.03), arr.pos = 1, arr.type = "triangle", lwd = 1) en.Node(c(x1, y3), lab = "u1") en.Node(c(x2, y3), lab = "u2") en.Node(c(x3, y2), lab = "u3", pos = 1.5) en.Node(c(x3, y4), lab = "u4", pos = 2.5) en.Node(c(x5, y4), lab = "u5") en.Capacitator(c(0.5*(x1 + x2),y3), lab = "C1", vert = FALSE) en.Capacitator(c(x4, y4), lab = "C3", vert = FALSE) en.Capacitator(c(x4, 0.5*(y1+y2)), lab = "C2", vert = TRUE) en.Resistor(c(x1, y2), lab = "R0") en.Resistor(c(x2, 0.5*(y1+y2)), lab = "R1") en.Resistor(c(x2, 0.5*(y4+y5)), lab = "R2") en.Resistor(c(x3, 0.5*(y4+y5)), lab = "R4") en.Resistor(c(x3, 0.5*(y1+y2)), lab = "R3") en.Resistor(c(x5, 0.5*(y1+y2)), lab = "R5") en.Ground(c(1.0, 0.05))## ============================================================================= ## en.Capacitator ## ============================================================================= emptyplot(main = "en.Capacitator") straightarrow(c(0.5, 0.9), c(0.5, 0.1), arr.pos = 0.3, arr.length = 0.25, arr.type = "triangle") en.Capacitator(c(0.5, 0.5), width = 0.075, length = 0.5, vert = TRUE) text(0.4, 0.65, "i", font = 3, cex = 2) straightarrow(c(0.8, 0.3), c(0.8, 0.77), arr.pos = 1, arr.length = 0.25, arr.type = "triangle", lwd = 1) text(0.925, 0.65, "v", font = 3, cex = 2) text(0.15, 0.5, "C", font = 3, cex = 2) box(col = "grey") ## ============================================================================= ## en.Resistor ## ============================================================================= emptyplot(main = "en.Resistor") straightarrow(c(0.5, 0.9), c(0.5, 0.1), arr.pos = 0.2, arr.length = 0.25, arr.type = "triangle", lwd = 1) text(0.4, 0.85, "i", font = 3, cex = 2) en.Resistor(c(0.5, 0.5), width = 0.25, length = 0.35 ) straightarrow(c(0.8, 0.3), c(0.8, 0.77), arr.pos = 1, arr.length = 0.25, arr.type = "triangle", lwd = 1) text(0.925, 0.65, "v", font = 3, cex = 2) text(0.5, 0.5, "R", font = 3, cex = 2) box(col = "grey") ## ============================================================================= ## en.Signal ## ============================================================================= emptyplot(main = "voltage source, en.Signal") lines(c(0.5, 0.5), c(0.1, 0.9)) en.Signal(c(0.5, 0.5), r = 0.15) straightarrow(c(0.8, 0.3), c(0.8, 0.77), arr.pos = 1, arr.length = 0.25, arr.type = "triangle", lwd = 1) text(0.925, 0.65, "v", font = 3, cex = 2) box(col = "grey") ## ============================================================================= ## en.Ground ## ============================================================================= emptyplot(main = "en.Ground") straightarrow(c(0.5, 0.7), c(0.5, 0.25), arr.pos = 1.0, arr.length = 0.25, arr.type = "triangle", lwd = 1) en.Ground(c(0.5, 0.65), width = 0.25, length = 0.35 ) box(col = "grey") ## ============================================================================= ## en.Node ## ============================================================================= emptyplot(main = "en.Node") rect(0.2, 0.2, 0.8, 0.8) en.Node(c(0.2, 0.2), lab = "N1" , pos = 1.5) en.Node(c(0.2, 0.8), lab = "N2" , pos = 2.5) en.Node(c(0.8, 0.8), lab = "N3" , pos = 3.5) en.Node(c(0.8, 0.2), lab = "N2" , pos = 4.5) box(col = "grey") ## ============================================================================= ## en.Amplifier example ## ============================================================================= emptyplot(main = "en.Amplifier") en.Amplifier(c(0.5, 0.5), r = 0.15) box(col = "grey") ## ============================================================================= ## en.Transistor example ## ============================================================================= emptyplot(main = "enTransistor") gate <- c(0.1, 0.5) mid <- c(0.5, 0.5) drain <- c(0.9, 0.9) source <- c(0.9, 0.1) en.Transistor(mid = mid, gate = gate, drain = drain, source = source, r = 0.15) text(0.2, 0.4, "Gate", font = 3) text(0.8, 0.9, "Drain", font = 3, adj = 1) text(0.8, 0.1, "Source", font = 3, adj = 1) box(col = "grey") ## ============================================================================= ## position of text examples ## ============================================================================= mf <- par (mfrow = c(2, 2)) openplotmat(main = "pos") segments(0, 0.5, 1, 0.5) for (i in 4:0) en.Resistor( mid = c(0.5, 0.5), width = 0.25, length = 0.25, lab = i, pos = i, dtext = 0.2) openplotmat(main = "pos") segments(0, 0.5, 1, 0.5) for (i in 1:4) en.Resistor( mid = c(0.5, 0.5), width = 0.25, length = 0.25, lab = i+0.5, pos = i+0.5, dtext = 0.25) openplotmat(main = "vert = TRUE") segments(0.5, 0, 0.5, 1) for (i in 1:4) en.Resistor( mid = c(0.5, i/5), width = 0.075, length = 0.125, lab = substitute(R[i], list(i = i) )) openplotmat(main = "vert = FALSE") segments(0, 0.5, 1, 0.5) for (i in 1:4) en.Resistor( mid = c(i/5, 0.5), width = 0.075, length = 0.125, lab = substitute(R[i], list(i = i) ), vert = FALSE) par(mfrow = mf) ## ============================================================================= ## A small transistor example ## ============================================================================= par(lwd = 1.5) par(mar = c(0, 0, 2, 0)) emptyplot(main = "transistor Amplifier", ylim = c(-0.1, 1), xlim = c(-0.1, 1.1), asp = FALSE) x1 <- 0; x2 <- 0.2; x3 <- 0.4; x4 <- 0.6; x5 <- 0.8; x6 <- 1; y1 <- 0.05; y2 <- 0.4; y3 <- 0.5; y4 <- 0.6; y5 <- 0.95 x23 <- (x2 + x3)/2 x56 <- (x5 + x6)/2 lines(c(x2, x6, x6, x2, x2, x1, x1, x23, x3, x3), c(y1, y1, y5, y5, y1, y1, y3, y3, y4, y5)) lines(c(x3, x3), c(y2, y1)) lines(c(x3, x4, x4), c(y2, y2, y1)) lines(c(x3, x5, x5), c(y4, y4, y1)) en.Transistor(mid = c(x23, y3), gate = c(x2, y3), drain = c(x3,y4), source = c(x3,y2), r = 0.035) en.Signal(c(x1, 0.2), lab = expression("U"["in"])) en.Signal(c(x6, y2), lab = expression("U"["b"])) straightarrow(c(x1 - 0.05, 0.23), c(x1 - 0.05, 0.17), arr.pos =1, arr.type = "triangle", lwd = 1) straightarrow(c(x6 + 0.05, y2 + 0.03), c(x6 + 0.05, y2 - 0.03), arr.pos = 1, arr.type = "triangle", lwd = 1) en.Node(c(x1, y3), lab = "u1") en.Node(c(x2, y3), lab = "u2") en.Node(c(x3, y2), lab = "u3", pos = 1.5) en.Node(c(x3, y4), lab = "u4", pos = 2.5) en.Node(c(x5, y4), lab = "u5") en.Capacitator(c(0.5*(x1 + x2),y3), lab = "C1", vert = FALSE) en.Capacitator(c(x4, y4), lab = "C3", vert = FALSE) en.Capacitator(c(x4, 0.5*(y1+y2)), lab = "C2", vert = TRUE) en.Resistor(c(x1, y2), lab = "R0") en.Resistor(c(x2, 0.5*(y1+y2)), lab = "R1") en.Resistor(c(x2, 0.5*(y4+y5)), lab = "R2") en.Resistor(c(x3, 0.5*(y4+y5)), lab = "R4") en.Resistor(c(x3, 0.5*(y1+y2)), lab = "R3") en.Resistor(c(x5, 0.5*(y1+y2)), lab = "R5") en.Ground(c(1.0, 0.05))
Creates a plotting region, bounded by [0,1] without axes, labels, titles
openplotmat (asp = NA, ...)openplotmat (asp = NA, ...)
asp |
the y/x aspect ratio. |
... |
arguments passed to |
Karline Soetaert <[email protected]>
emptyplot from package shape.
visualises a transition matrix as a number of (labeled) boxes connected by (labeled) arrows.
plotmat(A, pos = NULL, curve = NULL, name = NULL, absent = 0, relsize = 1, lwd = 2, lcol = "black", box.size = 0.1, box.type = "circle", box.prop = 1, box.col = "white", box.lcol = lcol, box.lwd = lwd, shadow.size = 0.01, shadow.col = "grey", dr = 0.01, dtext = 0.3, self.lwd = 1, self.cex = 1, self.shiftx = box.size, self.shifty = NULL, self.arrpos = NULL, arr.lwd = lwd, arr.lcol = lcol, arr.tcol = lcol, arr.col = "black", arr.type = "curved", arr.pos = 0.5, arr.length = 0.4, arr.width = arr.length/2, endhead = FALSE, mx = 0.0, my = 0.0, box.cex = 1, txt.col = "black", txt.xadj = 0.5, txt.yadj = 0.5, txt.font = 1, prefix = "", cex = 1, cex.txt = cex, add = FALSE, main = "", cex.main = cex, segment.from = 0, segment.to = 1, latex = FALSE, ...)plotmat(A, pos = NULL, curve = NULL, name = NULL, absent = 0, relsize = 1, lwd = 2, lcol = "black", box.size = 0.1, box.type = "circle", box.prop = 1, box.col = "white", box.lcol = lcol, box.lwd = lwd, shadow.size = 0.01, shadow.col = "grey", dr = 0.01, dtext = 0.3, self.lwd = 1, self.cex = 1, self.shiftx = box.size, self.shifty = NULL, self.arrpos = NULL, arr.lwd = lwd, arr.lcol = lcol, arr.tcol = lcol, arr.col = "black", arr.type = "curved", arr.pos = 0.5, arr.length = 0.4, arr.width = arr.length/2, endhead = FALSE, mx = 0.0, my = 0.0, box.cex = 1, txt.col = "black", txt.xadj = 0.5, txt.yadj = 0.5, txt.font = 1, prefix = "", cex = 1, cex.txt = cex, add = FALSE, main = "", cex.main = cex, segment.from = 0, segment.to = 1, latex = FALSE, ...)
A |
square coefficient matrix, specifying the links (rows=to, cols=from). |
pos |
vector, specifying the number of elements in each graph row, or a 2-column matrix with element position, or NULL. If a 2-column matrix, the values should be withing 0 and 1. |
curve |
one value, or a matrix, same dimensions as |
name |
string vector, specifying the names of elements, dimension =
number of rows (columns) of |
absent |
all elements in |
relsize |
scaling factor for size of the graph. |
lwd |
default line width of arrow and box. |
lcol |
default color of arrow line and box line. |
box.size |
size of label box, one value or a vector with dimension =
number of rows of |
box.type |
shape of label box (rect, ellipse, diamond, round, hexa,
multi), one value or a vector with dimension=number of rows of |
box.prop |
length/width ratio of label box, one value or a vector
with dimension=number of rows of |
box.col |
fill color of label box, one value or a vector with
dimension=number of rows of |
box.lcol |
line color of label box, one value or a vector with
dimension=number of rows of |
box.lwd |
line width of the box, one value or a vector with dimension
= number of rows of |
shadow.size |
relative size of shadow of label box, one value or a
vector with dimension=number of rows of |
shadow.col |
color of shadow of label box, one value or a vector with
dimension=number of rows of |
dr |
size of segments, in radians, to draw ellipse (decrease for smoother ellipses). |
dtext |
controls the position of arrow text relative to arrowhead. |
self.lwd |
line width of self-arrow, (arrow from i to i), one value or
a vector with dimension=number of rows of |
self.cex |
relative size of self-arrow, relative to box, one value or
a vector with dimension=number of rows of |
self.shiftx |
relative shift of self-arrow, in x-direction, one value
or a vector with dimension=number of rows of |
self.shifty |
relative shift of self-arrow, in y-direction, one value
or a vector with dimension=number of rows of |
self.arrpos |
position of the self-arrow, angle in radians relative to
x-direction, one value or a vector with dimension=number of rows of
|
arr.lwd |
line width of arrow, connecting two different points, one
value, or a matrix with same dimensions as |
arr.lcol |
color of arrow line, one value, or a matrix with same
dimensions as |
arr.tcol |
color of arrow text, one value, or a matrix with same
dimensions as |
arr.col |
color of arrowhead, one value, or a matrix with same
dimensions as |
arr.type |
type of arrowhead, one of ("curved", "triangle",
"circle", "ellipse", "T", "simple", "none"), one
value, or a matrix with same dimensions as |
arr.pos |
relative position of arrowhead on arrow segment/curve, one
value, or a matrix with same dimensions as |
arr.length |
arrow length, one value, or a matrix with same
dimensions as |
arr.width |
arrow width, one value, or a matrix with same dimensions
as |
endhead |
if TRUE: the arrow line stops at the arrowhead; default =
|
mx |
horizontal shift of the boxes. |
my |
vertical shift of the boxes. |
box.cex |
relative size of text in boxes, one value or a vector with
dimension=number of rows of |
txt.col |
color of text in boxes, one value or a vector with
dimension=number of rows of |
txt.xadj, txt.yadj
|
the x and y adjustment of the labels in the boxes,
one value or a vector with dimension=number of rows of |
txt.font |
the font to be used for the text in boxes,
one value or a vector with dimension=number of rows of |
prefix |
to be added in front of non-zero arrow labels. |
cex |
relative size of text. |
cex.txt |
relative size of arrow text, one value, or a matrix with
same dimensions as |
add |
start a new plot ( |
main |
main title. Only effective if |
cex.main |
relative size of main title. |
segment.from |
if not |
segment.to |
if not |
latex |
if |
... |
other arguments passed to function |
The square transition matrix A determines the number of elements
of A (rows of A) and which elements are connected
(all values in A different from absent).
A also provides the values of arrowlabels.
The position of the elements are specified with pos, which is
either NULL,
or a vector specifying the number of elements on a row, or a 2-columned
matrix specifying the (x,y) position of each element.
The ordering of elements is according to the row number of A
when pos is NULL, the elements will be arranged on a
circle
when pos is a vector, it specifies the number of elements in
each row.
For instance, with pos = c(3,2,1) the elements will be arranged
in 3 rows (length of vector); on top row, 3 elements; on second row 2,
and on third row 1 element will be positioned. All elements within a
row are equally distributed horizontally, all rows are equally
distributed vertically.
when pos is a matrix, it specifies the x (1st column) and y
(2nd column) position of each element.
The offset from x-axis and from y-axis can be changed with mx and
my.
The name of each element is given by vector name; this name is
written in its respective box.
The relative size of this text can be changed by box.cex.
By default, a shadow is drawn, in the right-lower corner of the box.
The shadow color and relative size is specified with shadow.col and
shadow.size respectively.
both can be one value (equal shadows) or a vector, specifying one value for each box shadow.
shadow.size = 0 toggles off the drawing of the shadow.
The type of the box is set with "box.type" which can take on the values:
"rect": a rectangle,
"ellipse": an ellipse,
"diamond": a diamond,
"round": a rectangle with rounded left and right edges,
"hexa": a hexagonal shape,
"multi": a multigonal shape.
"none" if no box is to be drawn.
The length of the box is set with box.size, the proportionality
(length/width) ratio with box.prop.
The fill-color of the box is specified with box.col;
the line width of the box with box.lwd and the line color with
box.lcol;
All box properties can be either one value (equal boxes) or a vector, specifying one value for each box.
For all values A[i,j] of A which are not equal to absent,
one arrow is drawn *from* column-element j *to* the row-element i of A.
The curvature of this arrow is specified with matrix element curve[i,j],
where 'curve' is either NULL, one value, or has the same dimension as A.
A straight arrow has curvature 0, NA (the default) chooses a default
curvature,
Positive or negative values of curve draws curved arrows.
If the arrow is curved, then dr is the increment used to draw the
ellipse; set to a lower value for smoother lines.
The type of the arrowhead is set with arr.type which can take the
values:
"simple" : uses comparable R function arrows
"triangle": uses filled triangle
"curved" : draws arrowhead with curved edges
"circle" : draws circular head
"ellipse" : draws ellepsoid head
"T" : draws T-shaped (blunt) head
"none" : no arrow head is drawn
The line color and width of the arrow line is set with arr.lcol and
arr.lwd
The size of the arrow head is specified with arr.length and
arr.width,
the position of the arrow head is specified with arr.pos (value
between [0,1]).
see Arrowhead for details on arrow head
a list containing:
arr |
a data.frame with arrow information:
. |
comp |
a matrix with the element position (centre of the boxes). |
radii |
the radiusses in x- and y-direction of the boxes. |
rect |
the "xleft","ybot","xright",and "ytop" of the boxes - redundant. |
Karline Soetaert <[email protected]>
Arrowhead from package shape
try: demo(plotmat)
M <- matrix(nrow = 4, ncol = 4, byrow = TRUE, data = 0) pp <- plotmat(M, pos = c(1, 2, 1), name = c("A", "B", "C", "D"), lwd = 1, box.lwd = 2, cex.txt = 0.8, box.size = 0.1, box.type = "square", box.prop = 0.5, main = "plotmat") pp # when explicitly given, pos should should be inbetween 0, 1 pos <- cbind (c(0.2, 0.4, 0.6, 0.8), c(0.8, 0.6, 0.4, 0.2)) pp <- plotmat(M, pos = pos, name = c("A", "B", "C", "D"), lwd = 1, box.lwd = 2, cex.txt = 0.8, box.size = 0.1, box.type = "square", box.prop = 0.5, main = "plotmat") # includes arrows between boxes pm <- par(mfrow = c(2, 2)) M <- matrix(nrow = 4, ncol = 4, byrow = TRUE, data = 0) M[2, 1] <- M[3, 1] <- M[4, 2] <- M[4, 3] <- "f1" col <- M col[] <- "red" col[2, 1] <- col[3, 1] <- "blue" pp <- plotmat(M, pos = c(1, 2, 1), curve = 0, name = 1:4, lwd = 1, box.lwd = 2, box.cex = 1:4, cex.txt = 0.8, arr.lcol = col, arr.tcol = col, arr.col = col, box.type = "circle", box.prop = 1.0, main = "plotmat") pp <- plotmat(M, pos = c(1, 2, 1), curve = 0, name = 1:4, lwd = 1, box.lwd = 2, box.cex = 1:4, cex.txt = 0.8, arr.lcol = col, arr.tcol = col, arr.col = col, box.type = "circle", box.prop = 1.0, arr.len = 0.3, segment.from = 0.35, segment.to = 0.65) M[1, 2] <- M[1, 3] <- M[2, 4] <- M[3, 4] <- "f2" pp <- plotmat(M, pos = c(1, 2, 1), curve = 0.1, name = 1:4, lwd = 1, box.lwd = 2, box.cex = 1:4, cex.txt = 0.8, arr.lcol = col, arr.tcol = col, arr.col = col, box.type = "none", box.prop = 1.0, main = "plotmat", arr.len = 0.2, segment.from = 0.3, segment.to = 0.7) pp <- plotmat(M, pos = c(1, 2, 1), curve = 0.1, name = 1:4, box.lwd = 2, box.cex = 1:4, cex.txt = 0.8, arr.lcol = col, arr.tcol = "green", arr.col = col, arr.pos = 0.7, arr.type = "simple", lwd = 2, box.type = "none", box.prop = 1.0, main = "plotmat", arr.len = 0.2, segment.from = 0.3, segment.to = 0.7) par(mfrow=pm) # self arrows diag(M) <- "self" pp <- plotmat(M, pos = c(2, 2), curve = 0, name = LETTERS[1:4], lwd = 1, box.lwd = 2, cex.txt = 0.8, self.cex = 0.5, self.shiftx = c(-0.1, 0.1, -0.1, 0.1), box.type = "diamond", box.prop = 0.5, main = "plotmat") # different arrows M <- matrix(nrow = 4, ncol = 4, data = 0) M[2, 1]<- 1 ; M[4, 2] <- 2 ; M[3, 4] <- 3; M[1, 3] <- 4 pp <- plotmat(M, pos = c(1, 2, 1), curve = 0.2, name = letters[1:4], lwd = 1, box.lwd = 2, cex.txt = 0.8, arr.type = "triangle", box.size = 0.1, box.type = "hexa", box.prop = 0.5, main = "plotmat") arrlwd <- M*2 arr.length <- M*0.4 cextxt <- M*0.8 plotmat(M, pos = c(1, 2, 1), curve = 0.2, name = letters[1:4], lwd = 1, box.lwd = 2, arr.type = "triangle", box.size = 0.1, box.type = "hexa", box.prop = 0.5, main = "plotmat", arr.lwd = arrlwd, arr.length = arr.length, cex.txt = cextxt, txt.font = 1:4, txt.xadj = seq(-3, 3, length.out = 4), txt.yadj = 1) M <- matrix(nrow = 4, ncol = 4, byrow = TRUE, data = 0) M <- as.data.frame(M) M[[2,1]]<- "k[si]" M[[3,1]]<- "k[N]" M[[4,2]]<- "sqrt(frac(2,3))" names <- c(expression(lambda[12]), "?", expression(lambda[13]),expression(lambda[23])) plotmat(M, pos = c(1, 2, 1), name = names, lwd = 1, box.lwd = 2, curve = 0, cex.txt = 0.8, box.size = 0.1, box.type = "square", box.prop = 0.5, main = "plotmat") plotmat(M, name = letters[1:4], curve = 0, box.cex = 1:4, box.lwd = 4:1, box.size = 0.075, arr.pos = 0.7, box.col = c("lightblue", "green", "yellow", "orange")) # No arrows, just lines with different colors M <- matrix(nrow = 4, ncol = 4, data = 0) M[2, 1]<- 1 ; M[4, 2] <- 2 ; M[3, 4] <- 3; M[1, 3] <- 4 pp <- plotmat(M, pos = c(1, 2, 1), curve = 0.2, name = letters[1:4], lwd = 1, box.lwd = 2, cex.txt = 0.8, arr.type = "none", arr.lcol = M, box.size = 0.1, box.type = "hexa", box.prop = 0.5, main = "plotmat") pp <- plotmat(M, pos = c(1, 2, 1), curve = 0.4, name = "", arr.type = "none", arr.lcol = M, box.type = "none", cex.txt = 0, main = "plotmat")M <- matrix(nrow = 4, ncol = 4, byrow = TRUE, data = 0) pp <- plotmat(M, pos = c(1, 2, 1), name = c("A", "B", "C", "D"), lwd = 1, box.lwd = 2, cex.txt = 0.8, box.size = 0.1, box.type = "square", box.prop = 0.5, main = "plotmat") pp # when explicitly given, pos should should be inbetween 0, 1 pos <- cbind (c(0.2, 0.4, 0.6, 0.8), c(0.8, 0.6, 0.4, 0.2)) pp <- plotmat(M, pos = pos, name = c("A", "B", "C", "D"), lwd = 1, box.lwd = 2, cex.txt = 0.8, box.size = 0.1, box.type = "square", box.prop = 0.5, main = "plotmat") # includes arrows between boxes pm <- par(mfrow = c(2, 2)) M <- matrix(nrow = 4, ncol = 4, byrow = TRUE, data = 0) M[2, 1] <- M[3, 1] <- M[4, 2] <- M[4, 3] <- "f1" col <- M col[] <- "red" col[2, 1] <- col[3, 1] <- "blue" pp <- plotmat(M, pos = c(1, 2, 1), curve = 0, name = 1:4, lwd = 1, box.lwd = 2, box.cex = 1:4, cex.txt = 0.8, arr.lcol = col, arr.tcol = col, arr.col = col, box.type = "circle", box.prop = 1.0, main = "plotmat") pp <- plotmat(M, pos = c(1, 2, 1), curve = 0, name = 1:4, lwd = 1, box.lwd = 2, box.cex = 1:4, cex.txt = 0.8, arr.lcol = col, arr.tcol = col, arr.col = col, box.type = "circle", box.prop = 1.0, arr.len = 0.3, segment.from = 0.35, segment.to = 0.65) M[1, 2] <- M[1, 3] <- M[2, 4] <- M[3, 4] <- "f2" pp <- plotmat(M, pos = c(1, 2, 1), curve = 0.1, name = 1:4, lwd = 1, box.lwd = 2, box.cex = 1:4, cex.txt = 0.8, arr.lcol = col, arr.tcol = col, arr.col = col, box.type = "none", box.prop = 1.0, main = "plotmat", arr.len = 0.2, segment.from = 0.3, segment.to = 0.7) pp <- plotmat(M, pos = c(1, 2, 1), curve = 0.1, name = 1:4, box.lwd = 2, box.cex = 1:4, cex.txt = 0.8, arr.lcol = col, arr.tcol = "green", arr.col = col, arr.pos = 0.7, arr.type = "simple", lwd = 2, box.type = "none", box.prop = 1.0, main = "plotmat", arr.len = 0.2, segment.from = 0.3, segment.to = 0.7) par(mfrow=pm) # self arrows diag(M) <- "self" pp <- plotmat(M, pos = c(2, 2), curve = 0, name = LETTERS[1:4], lwd = 1, box.lwd = 2, cex.txt = 0.8, self.cex = 0.5, self.shiftx = c(-0.1, 0.1, -0.1, 0.1), box.type = "diamond", box.prop = 0.5, main = "plotmat") # different arrows M <- matrix(nrow = 4, ncol = 4, data = 0) M[2, 1]<- 1 ; M[4, 2] <- 2 ; M[3, 4] <- 3; M[1, 3] <- 4 pp <- plotmat(M, pos = c(1, 2, 1), curve = 0.2, name = letters[1:4], lwd = 1, box.lwd = 2, cex.txt = 0.8, arr.type = "triangle", box.size = 0.1, box.type = "hexa", box.prop = 0.5, main = "plotmat") arrlwd <- M*2 arr.length <- M*0.4 cextxt <- M*0.8 plotmat(M, pos = c(1, 2, 1), curve = 0.2, name = letters[1:4], lwd = 1, box.lwd = 2, arr.type = "triangle", box.size = 0.1, box.type = "hexa", box.prop = 0.5, main = "plotmat", arr.lwd = arrlwd, arr.length = arr.length, cex.txt = cextxt, txt.font = 1:4, txt.xadj = seq(-3, 3, length.out = 4), txt.yadj = 1) M <- matrix(nrow = 4, ncol = 4, byrow = TRUE, data = 0) M <- as.data.frame(M) M[[2,1]]<- "k[si]" M[[3,1]]<- "k[N]" M[[4,2]]<- "sqrt(frac(2,3))" names <- c(expression(lambda[12]), "?", expression(lambda[13]),expression(lambda[23])) plotmat(M, pos = c(1, 2, 1), name = names, lwd = 1, box.lwd = 2, curve = 0, cex.txt = 0.8, box.size = 0.1, box.type = "square", box.prop = 0.5, main = "plotmat") plotmat(M, name = letters[1:4], curve = 0, box.cex = 1:4, box.lwd = 4:1, box.size = 0.075, arr.pos = 0.7, box.col = c("lightblue", "green", "yellow", "orange")) # No arrows, just lines with different colors M <- matrix(nrow = 4, ncol = 4, data = 0) M[2, 1]<- 1 ; M[4, 2] <- 2 ; M[3, 4] <- 3; M[1, 3] <- 4 pp <- plotmat(M, pos = c(1, 2, 1), curve = 0.2, name = letters[1:4], lwd = 1, box.lwd = 2, cex.txt = 0.8, arr.type = "none", arr.lcol = M, box.size = 0.1, box.type = "hexa", box.prop = 0.5, main = "plotmat") pp <- plotmat(M, pos = c(1, 2, 1), curve = 0.4, name = "", arr.type = "none", arr.lcol = M, box.type = "none", cex.txt = 0, main = "plotmat")
plots a web, based on a flow matrix
plotweb(flowmat, names = NULL, lab.size = 1.5, add = FALSE, fig.size = 1.3, main = "", sub = "", sub2 = "", log = FALSE, mar = c(2, 2, 2, 2), nullflow = NULL, minflow = NULL, maxflow = NULL, legend = TRUE, leg.digit = 5, leg.title = NULL, lcol = "black", arr.col = "black", val = FALSE, val.digit = 5, val.size = 0.6, val.col = "red", val.title = NULL, val.ncol = 1, budget = FALSE, bud.digit = 5, bud.size = 0.6, bud.title = "budget", bud.ncol = 1, maxarrow = 10, minarrow = 1, length = 0.1, dcirc = 1.2, bty = "o", ...)plotweb(flowmat, names = NULL, lab.size = 1.5, add = FALSE, fig.size = 1.3, main = "", sub = "", sub2 = "", log = FALSE, mar = c(2, 2, 2, 2), nullflow = NULL, minflow = NULL, maxflow = NULL, legend = TRUE, leg.digit = 5, leg.title = NULL, lcol = "black", arr.col = "black", val = FALSE, val.digit = 5, val.size = 0.6, val.col = "red", val.title = NULL, val.ncol = 1, budget = FALSE, bud.digit = 5, bud.size = 0.6, bud.title = "budget", bud.ncol = 1, maxarrow = 10, minarrow = 1, length = 0.1, dcirc = 1.2, bty = "o", ...)
flowmat |
flow matrix, rows=flow *from*, columns=flow *to*. |
names |
string vector with the names of components. |
lab.size |
relative size of name label text. |
add |
start a new plot ( |
fig.size |
if |
main |
if |
sub |
if |
sub2 |
if |
log |
logical indicating whether to scale the flow values logarithmically. |
mar |
the figure margins. |
nullflow |
either one value or a two-valued vector; if flow < nullflow[1] or flow > nullflow[2] (if two values): flow is assumed = 0 and the arrow is not drawn. |
minflow |
flowvalue corresponding to minimum arrow thickness. |
maxflow |
flowvalue corresponding to maximum arrow thickness. |
legend |
logical indicating whether to add a legend with arrow thickness. |
leg.digit |
nr of digits for writing legend - only if |
leg.title |
title for arrow legend, e.g to give units - only if
|
lcol |
line color of arrow - not used. |
arr.col |
arrow color. One value or a matrix, with same dimensions as flowmat; if a matrix, each arrow can have a different color. |
val |
logical indicating whether to write flow values as a legend. |
val.digit |
nr of digits for writing values - only if |
val.size |
relative size for writing values - only if |
val.col |
color for writing values - only if |
val.title |
title for values legend - only if |
val.ncol |
number of columns for writing values - only if
|
budget |
logical indicating whether to calculate budget (sum of flows in - sum of flows out) per component. |
bud.digit |
nr of digits for writing budget - only if
|
bud.size |
relative size for writing budget - only if
|
bud.title |
title for budget legend - only if
|
bud.ncol |
number of columns for writing budget - only if
|
maxarrow |
maximal thickness of arrow. |
minarrow |
minimal thickness of arrow. |
length |
length of the edges of the arrow head (in inches). |
dcirc |
if cannibalism (flow from i to i), offset of circular 'arrow' -
if |
bty |
the type of box to be drawn around the legends ( |
... |
extra arguments passed to R-function arrows. |
This function is less flexible than function plotmat
It is meant for visualisation of food web flows, that are inputted as a flow matrix.
It displays the elements on a circle, and, where there is a mass flow, two elements are connected,
the magnitude of the web flows is reflected by the thickness of the arrow
Note that the input matrices from function plotmat and plotweb
are transposed.
Karline Soetaert <[email protected]>
try: demo(plotweb)
plotweb(Rigaweb, main = "Gulf of Riga food web", sub = "mgC/m3/d", val = TRUE) ArrCol <- Rigaweb ArrCol[] <- "black" ArrCol[,"Sedimentation"] <- "green" plotweb(Rigaweb, main = "Gulf of Riga food web", sub = "mgC/m3/d", val = FALSE, arr.col = ArrCol) plotweb(diag(20), main = "plotweb")plotweb(Rigaweb, main = "Gulf of Riga food web", sub = "mgC/m3/d", val = TRUE) ArrCol <- Rigaweb ArrCol[] <- "black" ArrCol[,"Sedimentation"] <- "green" plotweb(Rigaweb, main = "Gulf of Riga food web", sub = "mgC/m3/d", val = FALSE, arr.col = ArrCol) plotweb(diag(20), main = "plotweb")
Carbon flux matrix of the Gulf of Riga planktonic food web in autumn as reconstructed by inverse modelling by Donali et al. (1999).
The Gulf of Riga is a highly eutrophic system in the Baltic Sea.
The foodweb comprises 7 functional compartments:
picoautotrophs (P1)
non-picoautotrophs (P2)
bacteria (B)
heterotrophic nanoflagellates (N)
zooplankton (Z)
detritus, including virus (D)
dissolved organic carbon (DOC)
and two external compartments:
CO2
Sedimentation
These compartments are connected with 26 flows.
Units of the flows are mg C/m3/day.
RigawebRigaweb
matrix with flow values, where element ij denotes flow from compartment i to j
rownames and columnames are the components.
Karline Soetaert <[email protected]>
Donali, E., Olli, K., Heiskanen, A.S., Andersen, T., 1999. Carbon flow patterns in the planktonic food web of the Gulf of Riga, the Baltic Sea: a reconstruction by the inverse method. Journal of Marine Systems 23, pp. 251 268.
plotweb(Rigaweb, main = "Gulf of Riga planktonic food web", sub = "mgC/m3/day")plotweb(Rigaweb, main = "Gulf of Riga planktonic food web", sub = "mgC/m3/day")
Connects two points with 3 segments (default = left-vertical-right) and adds an arrowhead on one of the segments at a certain distance
segmentarrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, arr.side = 2, arr.pos = 0.5, path = "LVR", dd = 0.5, ...)segmentarrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, arr.side = 2, arr.pos = 0.5, path = "LVR", dd = 0.5, ...)
from |
coordinates (x,y) of point *from* which to draw arrow. |
to |
coordinates (x,y) of point *to* which to draw arrow. |
lwd |
line width. |
lty |
line type. |
lcol |
line color. |
arr.col |
arrow color. |
arr.side |
segment number on which arrowhead is drawn (1,2,3). |
arr.pos |
relative position of arrowhead on segment on which arrowhead is drawn. |
path |
outline of the 3 segments, default: left, vertical, right. |
dd |
length of segment arm, directed away from endpoints. |
... |
arguments passed to function straightarrow. |
one segmented arrow is drawn between two points '(from, to)'
how the segments are drawn is set with path which can take on the
values:
"LVR": first left then vertical then right.
"RVL": first right then vertical then left.
"UHD": first up then horizontal then down.
"DHU": first down then horizontal then up.
The segment(s) on which the arrow head is drawn is set with arr.side,
which is one or more values in (1, 2, 3).
The position of the arrowhead, on the segment on which it is drawn,
is set with arr.pos, a value between 0(start of segment) and 1
(end of segment)
The type of the arrowhead is set with arr.type which can take
the values:
"none" : skips the drawing of arrows.
"simple" : uses comparable R function arrows.
"triangle": uses filled triangle.
"curved" : draws arrowhead with curved edges.
"circle" : draws circular head.
"ellipse" : draws ellepsoid head.
"T" : draws T-shaped (blunt) head.
The size of the arrow head can be specified with the arguments
arr.length and arr.width.
See Arrowhead from package shape for details on
arrow head.
coordinates (x,y) where arrowhead is drawn
Karline Soetaert <[email protected]>
straightarrow, bentarrow,
curvedarrow,
selfarrow, treearrow, splitarrow,
arrows: the comparable R function,
Arrows: more complicated arrow function from package
shape
try: demo(plotweb)
openplotmat(main="segmentarrow") pos <-cbind(A <- seq(0.2, 0.8, by = 0.2), rev(A)) text(pos, LETTERS[1:4], cex = 2) segmentarrow(from = pos[1, ] + c(0, 0.05), to = pos[2, ] + c(0, 0.05), arr.pos = 1, arr.adj = 1, dd = 0.1, path = "UHD", lcol = "darkred") segmentarrow(from = pos[2, ] + c(-0.05, 0), to = pos[3, ] + c(-0.05, 0.01), arr.pos = 1, arr.adj = 1, dd = 0.1, lcol = "black", arr.type = "triangle") segmentarrow(from = pos[2, ] + c(0.05, 0), to = pos[3, ] + c(0.05, 0.01), arr.pos = 0.5, dd = 0.3, path = "RVL", arr.side = 1, lcol = "lightblue", arr.type = "simple") segmentarrow(from = pos[3, ] + c(0.05, 0), to = pos[4, ] + c(-0.05, 0.01), arr.pos = 0.5, dd = 0.05, path = "RVL", lcol = "darkblue", arr.type = "ellipse") segmentarrow(from = pos[3, ] + c(0, -0.05), to = pos[4, ] + c(0, 0.05), arr.pos = 0.5, arr.side = 3, dd = 0.05, path = "DHU", lcol = "darkgreen") segmentarrow(from = pos[3,] + c(-0.05, -0.05), to = pos[4, ] + c(0, -0.05), arr.pos = 0.5, arr.side = 1:3, dd = 0.3, path = "DHU", lcol = "green")openplotmat(main="segmentarrow") pos <-cbind(A <- seq(0.2, 0.8, by = 0.2), rev(A)) text(pos, LETTERS[1:4], cex = 2) segmentarrow(from = pos[1, ] + c(0, 0.05), to = pos[2, ] + c(0, 0.05), arr.pos = 1, arr.adj = 1, dd = 0.1, path = "UHD", lcol = "darkred") segmentarrow(from = pos[2, ] + c(-0.05, 0), to = pos[3, ] + c(-0.05, 0.01), arr.pos = 1, arr.adj = 1, dd = 0.1, lcol = "black", arr.type = "triangle") segmentarrow(from = pos[2, ] + c(0.05, 0), to = pos[3, ] + c(0.05, 0.01), arr.pos = 0.5, dd = 0.3, path = "RVL", arr.side = 1, lcol = "lightblue", arr.type = "simple") segmentarrow(from = pos[3, ] + c(0.05, 0), to = pos[4, ] + c(-0.05, 0.01), arr.pos = 0.5, dd = 0.05, path = "RVL", lcol = "darkblue", arr.type = "ellipse") segmentarrow(from = pos[3, ] + c(0, -0.05), to = pos[4, ] + c(0, 0.05), arr.pos = 0.5, arr.side = 3, dd = 0.05, path = "DHU", lcol = "darkgreen") segmentarrow(from = pos[3,] + c(-0.05, -0.05), to = pos[4, ] + c(0, -0.05), arr.pos = 0.5, arr.side = 1:3, dd = 0.3, path = "DHU", lcol = "green")
adds a circular arrow, from and to the same point
selfarrow(pos, lwd = 2, lty = 1, lcol = "black", arr.pos = 0.5, path = "L", curve = c(0.1, 0.1), dr = 0.01, code = 1, ...)selfarrow(pos, lwd = 2, lty = 1, lcol = "black", arr.pos = 0.5, path = "L", curve = c(0.1, 0.1), dr = 0.01, code = 1, ...)
pos |
2-valued vector with coordinates (x,y) of points *from and to* which to draw arrow. |
lwd |
line width. |
lty |
line type. |
lcol |
line color. |
arr.pos |
relative position of arrowhead. |
path |
position of circle: R, L, U, D for right, left, up and down respectively. |
curve |
relative size of curve (fraction of arrow length). |
dr |
size of segments, in radians, to draw ellipse (decrease for smoother). |
code |
how to put the arrowhead. |
... |
arguments passed to function Arrows. |
draws a circular arrow from and to one point
The position of the arrowhead on the circle is set with arr.pos,
a value between 0 (at start) and 1(at end of circle)
The type of the arrowhead is set with arr.type which can take the
values:
"none" : skips the drawing of arrows.
"simple" : uses comparable R function arrows.
"triangle": uses filled triangle.
"curved" : draws arrowhead with curved edges.
"circle" : draws circular head.
"ellipse" : draws ellepsoid head.
"T" : draws T-shaped (blunt) head.
The size of the arrow head can be specified with the arguments
arr.length and arr.width.
See Arrowhead for details on arrow head.
coordinates (x,y) where arrowhead is drawn
Karline Soetaert <[email protected]>
straightarrow, segmentarrow,
curvedarrow,
bentarrow,treearrow, splitarrow,
arrows: the comparable R function,
Arrows: more complicated arrow function from package
shape.
openplotmat(main = "selfarrow") pos <- coordinates(3, mx = 0.05) text(pos, LETTERS[1:3], cex = 2) for (i in 1:3) selfarrow(pos = pos[i, ], path = "R", arr.pos = 0.2, curve = c(0.05, 0.1), lcol = "darkred") for (i in 1:3) selfarrow(pos = pos[i, ], path = "L", arr.pos = 0.7, lcol = "darkblue", curve = c(0.05, 0.05)) for (i in 1:3) selfarrow(pos = pos[i, ], path = "L", arr.pos = 0.5, lcol = "darkgreen", code = i, arr.type = "triangle")openplotmat(main = "selfarrow") pos <- coordinates(3, mx = 0.05) text(pos, LETTERS[1:3], cex = 2) for (i in 1:3) selfarrow(pos = pos[i, ], path = "R", arr.pos = 0.2, curve = c(0.05, 0.1), lcol = "darkred") for (i in 1:3) selfarrow(pos = pos[i, ], path = "L", arr.pos = 0.7, lcol = "darkblue", curve = c(0.05, 0.05)) for (i in 1:3) selfarrow(pos = pos[i, ], path = "L", arr.pos = 0.5, lcol = "darkgreen", code = i, arr.type = "triangle")
adds a box, with shadow on a plot; used for writing text
shadowbox(box.type = "rect", mid, radx, rady = radx, shadow.size = 0.01, shadow.col = "grey", box.col = "white", lcol = "black", lwd = 1, dr = 0.01, angle = 0, len = 1, nr = 5, rx = rady, theta = 90, ...)shadowbox(box.type = "rect", mid, radx, rady = radx, shadow.size = 0.01, shadow.col = "grey", box.col = "white", lcol = "black", lwd = 1, dr = 0.01, angle = 0, len = 1, nr = 5, rx = rady, theta = 90, ...)
box.type |
shape of the box. |
mid |
midpoint (x,y) of the box. |
radx |
horizontal radius of the box. |
rady |
vertical radius of the box. |
shadow.size |
relative size of shadow. |
shadow.col |
color of shadow. |
box.col |
fill color of the box. |
lcol |
line color surrounding box. |
lwd |
line width of line surrounding the box. |
dr |
if box is curved: size of segments, in radians, to draw ellipse (decrease for smoother). |
angle |
rotation angle, degrees. |
len |
if |
nr |
if |
rx |
if |
theta |
if |
... |
other arguments. |
one box is drawn, centered aroung point mid and with horizontal and
vertical radiusses radx, rady.
By default, a shadow is drawn, in the right-lower corner of the box.
The shadow color and relative size is specified with shadow.col and
shadow.size respectively.
shadow.size = 0 toggles off the drawing of the shadow.
the type of the box is set with box.type which can take on the values:
"rect": a rectangle.
"ellipse": an ellipse.
"diamond": a diamond.
"round": a rectangle with rounded sides.
"hexa": a hexagonal shape.
"multi": a multigonal shape; also input "nr", the number of angles.
"cylinder": a cylindrical shape; also input "len", the length of the cylinder.
"parallel": a parallelogram; “theta” is the angle of the bottom left corner.
the fill-color of the box is specified with box.col;
the line width and color of the box are specified with lwd and
lcol
Karline Soetaert <[email protected]>
openplotmat(main="shadowbox") shadowbox(box.type = "rect", mid = c(0.1, 0.5), rady = 0.1, radx = 0.05, angle = 25) shadowbox(box.type = "round", mid = c(0.3, 0.5), rady = 0.05, radx = 0.025, angle = 90, shadow.col = "darkred") shadowbox(box.type = "ellipse", mid = c(0.5, 0.5), rady = 0.05, radx = 0.075, box.col = "blue") shadowbox(box.type = "multi", mid = c(0.8, 0.5), rady = 0.05, radx = 0.05, box.col = "darkblue", nr = 5)openplotmat(main="shadowbox") shadowbox(box.type = "rect", mid = c(0.1, 0.5), rady = 0.1, radx = 0.05, angle = 25) shadowbox(box.type = "round", mid = c(0.3, 0.5), rady = 0.05, radx = 0.025, angle = 90, shadow.col = "darkred") shadowbox(box.type = "ellipse", mid = c(0.5, 0.5), rady = 0.05, radx = 0.075, box.col = "blue") shadowbox(box.type = "multi", mid = c(0.8, 0.5), rady = 0.05, radx = 0.05, box.col = "darkblue", nr = 5)
connects two sets of points with a star-like structure, adds an arrowhead at a certain distance
splitarrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, arr.side = 2, arr.pos = 0.5, centre = NULL, dd = 0.5, ...)splitarrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, arr.side = 2, arr.pos = 0.5, centre = NULL, dd = 0.5, ...)
from |
matrix of coordinates (x,y) of points *from* which to draw arrow. |
to |
matrix of coordinates (x,y) of points *to* which to draw arrow. |
lwd |
line width. |
lty |
line type. |
lcol |
line color. |
arr.col |
arrow color. |
arr.side |
segment number on which arrowhead is drawn (1,2). |
arr.pos |
relative position of arrowhead on segment on which arrowhead is drawn. |
centre |
coordinates (x,y) of central point. |
dd |
relative position of central point, only when |
... |
other arguments passed to function straightarrow. |
a branched arrow is drawn between points '(from, to)',
where both from and to can be several points.
The arrow segments radiate into a central point. Either the (x,y)
coordinates of this central point are set with centre or
it is estimated at a certain distance (dd >0,<1) between the
centroid of the *from* points and the centroid of the *to*
points.
The segment(s) on which the arrow head is drawn is set with arr.side,
which is one or more values in (1, 2)
arr.side=1 sets the arrow head on the segment *from* ->
central point
arr.side=2 sets the arrow head on the segment
central point -> *to*
The position of the arrowhead on the segment on which it is drawn,
is set with arr.pos, a value between 0(start of segment) and
1(end of segment)
The type of the arrowhead is set with arr.type which can take the
values:
"none" : skips the drawing of arrows.
"simple" : uses comparable R function arrows.
"triangle": uses filled triangle.
"curved" : draws arrowhead with curved edges.
"circle" : draws circular head.
"ellipse" : draws ellepsoid head.
"T" : draws T-shaped (blunt) head.
The size of the arrow head can be specified with the arguments
arr.length and arr.width.
See Arrowhead from package shape for details on
arrow head.
coordinates (x,y) where arrowheads are drawn
Karline Soetaert <[email protected]>
straightarrow, segmentarrow,
curvedarrow, selfarrow, bentarrow,
treearrow,
arrows: the comparable R function,
Arrows: more complicated arrow function from package
shape.
openplotmat(main = "splitarrow") pos <- coordinates(c(1, 2, 2, 4, 1)) splitarrow(from = pos[1, ], to = pos[2:10, ], arr.side = 1, centre = c(0.5, 0.625)) for (i in 1:10) textrect(pos[i, ], lab = i, cex = 2, radx = 0.05) openplotmat(main = "splitarrow") pos <- coordinates(c(1, 3)) splitarrow(from = pos[1,], to = pos[2:4, ], arr.side = 1) splitarrow(from = pos[1,], to = pos[2:4, ], arr.side = 2) for (i in 1:4) textrect(pos[i, ], lab = i, cex = 2, radx = 0.05) openplotmat(main = "splitarrow") pos <- coordinates(N = 6) pos <- rbind(c(0.5, 0.5), pos) splitarrow(from = pos[1, ], to = pos[2:7, ], arr.side = 2) for (i in 1:7) textrect(pos[i, ], lab = i, cex = 2, radx = 0.05)openplotmat(main = "splitarrow") pos <- coordinates(c(1, 2, 2, 4, 1)) splitarrow(from = pos[1, ], to = pos[2:10, ], arr.side = 1, centre = c(0.5, 0.625)) for (i in 1:10) textrect(pos[i, ], lab = i, cex = 2, radx = 0.05) openplotmat(main = "splitarrow") pos <- coordinates(c(1, 3)) splitarrow(from = pos[1,], to = pos[2:4, ], arr.side = 1) splitarrow(from = pos[1,], to = pos[2:4, ], arr.side = 2) for (i in 1:4) textrect(pos[i, ], lab = i, cex = 2, radx = 0.05) openplotmat(main = "splitarrow") pos <- coordinates(N = 6) pos <- rbind(c(0.5, 0.5), pos) splitarrow(from = pos[1, ], to = pos[2:7, ], arr.side = 2) for (i in 1:7) textrect(pos[i, ], lab = i, cex = 2, radx = 0.05)
Plots straight line between two points
adds an arrowhead at a certain distance.
straightarrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, arr.pos = 0.5, endhead = FALSE, segment = c(0,1), ...)straightarrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, arr.pos = 0.5, endhead = FALSE, segment = c(0,1), ...)
from |
coordinates (x,y) of the point *from* which to draw arrow. |
to |
coordinates (x,y) of the point *to* which to draw arrow. |
lwd |
line width. |
lty |
line type. |
lcol |
line color. |
arr.col |
arrow color. |
arr.pos |
relative position of arrowhead. |
endhead |
if |
segment |
if not |
... |
arguments passed to function Arrows. |
a straight arrow is drawn between the points '(from,
to)'
The position of the arrowhead, is set with arr.pos, a value between
0(start point) and 1(endpoint)
The type of the arrowhead is set with arr.type which can take
the values:
"none" : skips the drawing of arrows.
"simple" : uses comparable R function arrows.
"triangle": uses filled triangle.
"curved" : draws arrowhead with curved edges.
"circle" : draws circular head.
"ellipse" : draws ellepsoid head.
"T" : draws T-shaped (blunt) head.
The size of the arrow head can be specified with the arguments
arr.length and arr.width.
See Arrowhead from package shape for details on
arrow head.
coordinates (x,y) where arrowhead is drawn
Karline Soetaert <[email protected]>
bentarrow, segmentarrow, curvedarrow
selfarrow, splitarrow, treearrow,
arrows: the comparable R function,
Arrows: more complicated arrow function from package
shape.
openplotmat(main = "straightarrow") pos <- coordinates(c(2, 3, 1)) for (i in 1:5) straightarrow(from = pos[i, ], to = pos[i+1, ], arr.pos = 0.5) straightarrow(from = pos[6, ], to = pos[6, ] + c(0.3, 0.), arr.type = "T", arr.pos = 1, arr.lwd = 3) for (i in 1:6) textrect(pos[i, ], lab = LETTERS[i], radx = 0.05)openplotmat(main = "straightarrow") pos <- coordinates(c(2, 3, 1)) for (i in 1:5) straightarrow(from = pos[i, ], to = pos[i+1, ], arr.pos = 0.5) straightarrow(from = pos[6, ], to = pos[6, ] + c(0.3, 0.), arr.type = "T", arr.pos = 1, arr.lwd = 3) for (i in 1:6) textrect(pos[i, ], lab = LETTERS[i], radx = 0.05)
Carbon flux matrix of the Takapoto atoll planktonic food web
as reconstructed by inverse modelling by Niquil et al. (1998).
The Takapoto Atoll lagoon is located in the French Polynesia of the South Pacific
The food web comprises 7 functional compartments:
Phytoplankton
Bacteria
Protozoa
Microzooplankton
Mesozooplankton
Detritus
Dissolved organic carbon (DOC)
and three external compartments/sinks:
CO2
Sedimentation
Grazing
These compartments are connected with 32 flows. Units of the flows are mg C/m2/day
TakapotowebTakapotoweb
matrix with flow values, where element ij denotes flow from compartment i to j
rownames and columnames are the components.
Karline Soetaert <[email protected]>
Niquil, N., Jackson, G.A., Legendre, L., Delesalle, B., 1998. Inverse model analysis of the planktonic food web of Takapoto Atoll (French Polynesia). Marine Ecology Progress Series 165, pp. 17 29.
plotweb(Takapotoweb, main = "Takapoto atoll planktonic food web", sub = "mgC/m2/day", lab.size = 1)plotweb(Takapotoweb, main = "Takapoto atoll planktonic food web", sub = "mgC/m2/day", lab.size = 1)
Transition matrix of the population dynamics model of teasel (Dipsacus sylvestris), a European perennial weed, as discussed in Caswell (2001), and in Soetaert and Herman, (2009)
The life cycle of teasel can be described by six stages:
dormant seeds < 1yr (DS 1yr)
dormant seeds 1-2yr (DS 2yr)
small rosettes <2.5cm (R small)
medium rosettes 2.5-18.9 cm (R medium)
large rosettes >19 cm (R large)
flowering plants (F)
The matrix contains the transition probabilities from one compartment (column) to another (row).
TeaselTeasel
matrix with transition probabilities, where element ij denotes transition from compartment j to i
rownames and columnames are the component names
Karline Soetaert <[email protected]>
Caswell, H. 2001. Matrix population models: construction, analysis, and interpretation. Second edition. Sinauer, Sunderland, Mass.
Karline Soetaert and Peter Herman. 2009. A practical guide to ecological modelling. Using R as a simulation platform. Springer.
curves <- matrix(nrow = ncol(Teasel), ncol = ncol(Teasel), 0) curves[3,1] <- curves[1,6] <- -0.35 curves[4,6] <- curves[6,4] <- curves[5,6] <- curves[6,5] <- 0.08 curves[3,6] <- 0.35 plotmat(Teasel, pos = c(3, 2, 1), curve = curves, lwd = 1, box.lwd = 2, cex.txt = 0.8, box.cex = 0.8, box.size = 0.08, arr.length = 0.5, box.type = "circle", box.prop = 1, shadow.size = 0.01, self.cex = 0.6, my = -0.075, mx = -0.01, relsize = 0.9, self.shifty = 0, self.shiftx = c(0, 0, 0.125, -0.12, 0.125, 0), main = "Dispsacus sylvestris")curves <- matrix(nrow = ncol(Teasel), ncol = ncol(Teasel), 0) curves[3,1] <- curves[1,6] <- -0.35 curves[4,6] <- curves[6,4] <- curves[5,6] <- curves[6,5] <- 0.08 curves[3,6] <- 0.35 plotmat(Teasel, pos = c(3, 2, 1), curve = curves, lwd = 1, box.lwd = 2, cex.txt = 0.8, box.cex = 0.8, box.size = 0.08, arr.length = 0.5, box.type = "circle", box.prop = 1, shadow.size = 0.01, self.cex = 0.6, my = -0.075, mx = -0.01, relsize = 0.9, self.shifty = 0, self.shiftx = c(0, 0, 0.125, -0.12, 0.125, 0), main = "Dispsacus sylvestris")
adds one or more lines of text, in a diamond-shaped box.
textdiamond(mid, radx, rady = NULL, lwd = 1, shadow.size = 0.01, adj = c(0.5,0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, ...)textdiamond(mid, radx, rady = NULL, lwd = 1, shadow.size = 0.01, adj = c(0.5,0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, ...)
mid |
midpoint (x,y) of the box. |
radx |
horizontal radius of the box. |
rady |
vertical radius of the box. |
lwd |
line width of line surrounding the box. |
shadow.size |
relative size of shadow. |
adj |
text adjustment. |
lab |
one label or a vector string of labels to be added in box. |
box.col |
fill color of the box. |
lcol |
line color surrounding box. |
shadow.col |
color of shadow. |
angle |
rotation angle, degrees. |
... |
other arguments passed to function textplain. |
see shadowbox for specifications of the diamond-shaped box
and its shadow.
Karline Soetaert <[email protected]>
textellipse, textempty,texthexa,
textmulti, textplain, textrect,
textround
openplotmat(xlim = c(-0.1, 1.1), main = "textdiamond") for (i in 1:10) textdiamond(mid = runif(2), col = i, radx = 0.1, rady = 0.05, lab = LETTERS[i], cex = 2, angle = runif(1)*360)openplotmat(xlim = c(-0.1, 1.1), main = "textdiamond") for (i in 1:10) textdiamond(mid = runif(2), col = i, radx = 0.1, rady = 0.05, lab = LETTERS[i], cex = 2, angle = runif(1)*360)
adds one or more lines of text, centered around "mid" in an ellipsoid box
textellipse(mid, radx, rady = radx*length(lab), lwd = 1, shadow.size = 0.01, adj = c(0.5, 0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, dr = 0.01, ...)textellipse(mid, radx, rady = radx*length(lab), lwd = 1, shadow.size = 0.01, adj = c(0.5, 0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, dr = 0.01, ...)
mid |
midpoint (x,y) of the box. |
radx |
horizontal radius of the box. |
rady |
vertical radius of the box. |
lwd |
line width of line surrounding the box. |
shadow.size |
relative size of shadow. |
adj |
text adjustment. |
lab |
one label or a vector string of labels to be added in box. |
box.col |
fill color of the box. |
lcol |
line color surrounding box. |
shadow.col |
color of shadow. |
angle |
rotation angle, degrees. |
dr |
size of segments, in radians, to draw ellipse (decrease for smoother). |
... |
other arguments passed to function textplain. |
see shadowbox for specifications of the ellipsoid-shaped box
and its shadow
Karline Soetaert <[email protected]>
textdiamond, textempty, texthexa,
textmulti, textplain, textrect,
textround
openplotmat(xlim = c(-0.1, 1.1), main = "textellipse") for (i in 1:10) textellipse(mid = runif(2), col = i, box.col = grey(0.95), radx = 0.1, rady = 0.05, lab = LETTERS[i], cex = 2, angle = runif(1)*360)openplotmat(xlim = c(-0.1, 1.1), main = "textellipse") for (i in 1:10) textellipse(mid = runif(2), col = i, box.col = grey(0.95), radx = 0.1, rady = 0.05, lab = LETTERS[i], cex = 2, angle = runif(1)*360)
adds one or more lines of text, with a colored background, no box
textempty(mid, lab = "", adj = c(0.5, 0.5), box.col = "white", cex = 1, ...)textempty(mid, lab = "", adj = c(0.5, 0.5), box.col = "white", cex = 1, ...)
mid |
midpoint (x,y) of the text. |
lab |
one label or a vector string of labels to be added in box. |
adj |
text adjustment. |
box.col |
background color. |
cex |
relative size of text. |
... |
other arguments passed to function textplain. |
Karline Soetaert <[email protected]>
textdiamond, textellipse, texthexa,
textmulti, textplain, textrect,
textround
openplotmat(xlim = c(-0.1, 1.1), col = "lightgrey", main = "textempty") for (i in 1:10) textempty(mid = runif(2), box.col = i, lab = LETTERS[i], cex = 2) textempty(mid = c(0.5, 0.5), adj = c(0, 0), lab = "textempty", box.col = "white")openplotmat(xlim = c(-0.1, 1.1), col = "lightgrey", main = "textempty") for (i in 1:10) textempty(mid = runif(2), box.col = i, lab = LETTERS[i], cex = 2) textempty(mid = c(0.5, 0.5), adj = c(0, 0), lab = "textempty", box.col = "white")
adds one or more lines of text, centered around "mid" in an hexagonal box.
texthexa(mid, radx, rady = radx*length(lab), lwd = 1, shadow.size = 0.01, adj = c(0.5,0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, ...)texthexa(mid, radx, rady = radx*length(lab), lwd = 1, shadow.size = 0.01, adj = c(0.5,0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, ...)
mid |
midpoint (x,y) of the box. |
radx |
horizontal radius of the box. |
rady |
vertical radius of the box. |
lwd |
line width of line surrounding the box. |
shadow.size |
relative size of shadow. |
adj |
text adjustment. |
lab |
one label or a vector string of labels to be added in box. |
box.col |
fill color of the box. |
lcol |
line color surrounding box. |
shadow.col |
color of shadow. |
angle |
rotation angle, degrees. |
... |
other arguments passed to function textplain. |
see shadowbox for specifications of the hexangular box
and its shadow
Karline Soetaert <[email protected]>
textdiamond, textellipse, textempty,
textmulti, textplain, textrect,
textround
openplotmat(xlim = c(-0.1, 1.1), main = "texthexa") for (i in 1:20) texthexa(mid = runif(2), angle = runif(1)*360, col = i, box.col = grey(0.95), radx = 0.1, rady = 0.05, lab = LETTERS[i], cex = 2)openplotmat(xlim = c(-0.1, 1.1), main = "texthexa") for (i in 1:20) texthexa(mid = runif(2), angle = runif(1)*360, col = i, box.col = grey(0.95), radx = 0.1, rady = 0.05, lab = LETTERS[i], cex = 2)
adds one or more lines of text, centered around "mid" in an multigonal box
textmulti(mid, radx, rady = radx*length(lab), lwd = 1, shadow.size = 0.01, adj = c(0.5, 0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, nr = 6, ...)textmulti(mid, radx, rady = radx*length(lab), lwd = 1, shadow.size = 0.01, adj = c(0.5, 0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, nr = 6, ...)
mid |
midpoint (x,y) of the box. |
radx |
horizontal radius of the box. |
rady |
vertical radius of the box. |
lwd |
line width of line surrounding the box. |
shadow.size |
relative size of shadow. |
adj |
text adjustment. |
lab |
one label or a vector string of labels to be added in box. |
box.col |
fill color of the box. |
lcol |
line color surrounding box. |
shadow.col |
color of shadow. |
angle |
rotation angle, degrees. |
nr |
the number of angles. |
... |
other arguments passed to function textplain. |
see shadowbox for specifications of the multigonal box and
its shadow.
Karline Soetaert <[email protected]>
textdiamond, textellipse, textempty,
texthexa, textplain, textrect,
textround.
openplotmat(xlim = c(-0.1, 1.1), main = "textmulti") for (i in 1:10) textmulti(mid = runif(2), col = i, radx = 0.1, rady = 0.1, lab = LETTERS[i], cex = 2, nr = trunc(i/1.5)+3)openplotmat(xlim = c(-0.1, 1.1), main = "textmulti") for (i in 1:10) textmulti(mid = runif(2), col = i, radx = 0.1, rady = 0.1, lab = LETTERS[i], cex = 2, nr = trunc(i/1.5)+3)
adds one or more lines of text, centered around "mid"
textplain(mid, height = 0.1, lab = "", adj = c(0.5, 0.5), ...)textplain(mid, height = 0.1, lab = "", adj = c(0.5, 0.5), ...)
mid |
central coordinates where to write the text. |
height |
height of text. |
lab |
one or more character strings or expressions specifying the *text* to be written. |
adj |
label adjustments. |
... |
other arguments passed to R-function text. |
Karline Soetaert <[email protected]>
textdiamond, textellipse, textempty,
texthexa, textmulti, textrect,
textround
openplotmat(main = "textplain") textplain(mid = c(0.5, 0.5), lab = c("this text is", "centered", "4 strings", "on 4 lines")) textplain(mid = c(0.5, 0.2), adj = c(0, 0.5), font = 2, height = 0.05, lab = c("this text is","left alligned")) textplain(mid = c(0.5, 0.8), adj = c(1, 0.5), font = 3, height = 0.05, lab = c("this text is","right alligned"))openplotmat(main = "textplain") textplain(mid = c(0.5, 0.5), lab = c("this text is", "centered", "4 strings", "on 4 lines")) textplain(mid = c(0.5, 0.2), adj = c(0, 0.5), font = 2, height = 0.05, lab = c("this text is","left alligned")) textplain(mid = c(0.5, 0.8), adj = c(1, 0.5), font = 3, height = 0.05, lab = c("this text is","right alligned"))
Adds one or more lines of text, centered around "mid" in a rectangular box, or in a paralellogram
textrect(mid, radx, rady = radx*length(lab), lwd = 1, shadow.size = 0.01, adj = c(0.5, 0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, ...) textparallel (mid, radx, rady = radx*length(lab), lwd = 1, shadow.size = 0.01, adj = c(0.5, 0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, theta = 90, ...)textrect(mid, radx, rady = radx*length(lab), lwd = 1, shadow.size = 0.01, adj = c(0.5, 0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, ...) textparallel (mid, radx, rady = radx*length(lab), lwd = 1, shadow.size = 0.01, adj = c(0.5, 0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, theta = 90, ...)
mid |
midpoint (x,y) of the box. |
radx |
horizontal radius of the box. |
rady |
vertical radius of the box. |
lwd |
line width of line surrounding the box. |
shadow.size |
relative size of shadow. |
adj |
text adjustment. |
lab |
one label or a vector string of labels to be added in box. |
box.col |
fill color of the box. |
lcol |
line color surrounding box. |
shadow.col |
color of shadow. |
angle |
rotation angle, degrees. |
theta |
angle of the bottom, left corner of the parallelogram, in degrees. |
... |
other arguments passed to function textplain. |
see shadowbox for specifications of the rectangular box and
its shadow.
Karline Soetaert <[email protected]>
Thanks to Michael Folkes for the code of the parallelogram.
textdiamond, textellipse, textempty,
texthexa, textmulti, textplain,
textround
openplotmat(xlim = c(-0.1, 1.1), main = "textrect") for (i in 1:10) textrect(mid = runif(2), col = i, radx = 0.1, rady = 0.1, lab = LETTERS[i], cex = 2) openplotmat(xlim = c(-0.1, 1.1), main = "textparallel") elpos <-coordinates (c(1, 1, 1, 1, 1)) textparallel(mid = elpos[1,], col = 1, radx = 0.2, rady = 0.1, lab = "theta=20", theta = 20) textparallel(mid = elpos[2,], col = 1, radx = 0.2, rady = 0.1, lab = "theta=60", theta = 60) textparallel(mid = elpos[3,], col = 1, radx = 0.2, rady = 0.1, lab = "theta=100", theta = 100) textparallel(mid = elpos[4,], col = 1, radx = 0.2, rady = 0.1, lab = "theta=140", theta = 140) textparallel(mid = elpos[5,], col = 1, radx = 0.2, rady = 0.1, lab = "theta=170", theta = 170)openplotmat(xlim = c(-0.1, 1.1), main = "textrect") for (i in 1:10) textrect(mid = runif(2), col = i, radx = 0.1, rady = 0.1, lab = LETTERS[i], cex = 2) openplotmat(xlim = c(-0.1, 1.1), main = "textparallel") elpos <-coordinates (c(1, 1, 1, 1, 1)) textparallel(mid = elpos[1,], col = 1, radx = 0.2, rady = 0.1, lab = "theta=20", theta = 20) textparallel(mid = elpos[2,], col = 1, radx = 0.2, rady = 0.1, lab = "theta=60", theta = 60) textparallel(mid = elpos[3,], col = 1, radx = 0.2, rady = 0.1, lab = "theta=100", theta = 100) textparallel(mid = elpos[4,], col = 1, radx = 0.2, rady = 0.1, lab = "theta=140", theta = 140) textparallel(mid = elpos[5,], col = 1, radx = 0.2, rady = 0.1, lab = "theta=170", theta = 170)
adds one or more lines of text, centered around "mid" in an a rectangular box with rounded sides
textround(mid, radx, rady = radx*length(lab), lwd = 1, shadow.size = 0.01, adj = c(0.5, 0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, rx = rady, ...)textround(mid, radx, rady = radx*length(lab), lwd = 1, shadow.size = 0.01, adj = c(0.5, 0.5), lab = "", box.col = "white", lcol = "black", shadow.col = "grey", angle = 0, rx = rady, ...)
mid |
midpoint (x,y) of the box. |
radx |
horizontal radius of the box. |
rady |
vertical radius of the box. |
lwd |
line width of line surrounding the box. |
shadow.size |
relative size of shadow. |
adj |
text adjustment. |
lab |
one label or a vector string of labels to be added in box. |
box.col |
fill color of the box. |
lcol |
line color surrounding box. |
shadow.col |
color of shadow. |
angle |
rotation angle, degrees. |
rx |
the radius of the rounded part. |
... |
other arguments passed to function textplain. |
see shadowbox for specifications of the box and its shadow
Karline Soetaert <[email protected]>
textdiamond, textellipse, textempty,
texthexa, textmulti, textplain,
textrect.
openplotmat(xlim = c(-0.1, 1.1), main = "textround") for (i in 1:10) textround(mid = runif(2), col = i, radx = 0.03, rady = 0.075, lab = LETTERS[i], cex = 2)openplotmat(xlim = c(-0.1, 1.1), main = "textround") for (i in 1:10) textround(mid = runif(2), col = i, radx = 0.03, rady = 0.075, lab = LETTERS[i], cex = 2)
connects two sets of points with a dendrogram-like structure,
adds an arrowhead at a certain distance.
treearrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, arr.side = 2, arr.pos = 0.5, line.pos = 0.5, path = "H", ...)treearrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, arr.side = 2, arr.pos = 0.5, line.pos = 0.5, path = "H", ...)
from |
matrix of coordinates (x,y) of points *from* which to draw arrow. |
to |
matrix of coordinates (x,y) of points *to* which to draw arrow. |
lwd |
line width. |
lty |
line type. |
lcol |
line color. |
arr.col |
arrow color. |
arr.side |
segment number on which arrowhead is drawn (1,2). |
arr.pos |
relative position of arrowhead on segment on which arrowhead is drawn. |
line.pos |
relative position of (horizontal/vertical) line. |
path |
Vertical, Horizontal. |
... |
other arguments passed to function straightarrow. |
a tree-shaped arrow is drawn between points '(from, to)',
where both from and to can be several points.
How the segments are drawn is set with path which can take on the
values:
"H": (horizontal): first left or right.
"V": (vertical): first down- or upward.
The segment(s) on which the arrow head is drawn is set with arr.side,
which is one or more values in (1, 2)
The position of the arrowhead on the segment on which it is drawn,
is set with arr.pos, a value between 0(start of segment) and
1(end of segment)
The type of the arrowhead is set with arr.type which can take the
values:
"none" : skips the drawing of arrows.
"simple" : uses comparable R function arrows.
"triangle": uses filled triangle.
"curved" : draws arrowhead with curved edges.
"circle" : draws circular head.
"ellipse" : draws ellepsoid head.
"T" : draws T-shaped (blunt) head.
The size of the arrow head can be specified with the arguments
arr.length and arr.width.
See Arrowhead from package shape for details
on arrow head.
coordinates (x,y) where arrowhead is drawn
Karline Soetaert <[email protected]>
straightarrow, segmentarrow,
curvedarrow, selfarrow,
bentarrow, splitarrow,
arrows: the comparable R function,
Arrows: more complicated arrow function from package
shape.
openplotmat(main = "treearrow") pos <- coordinates(c(3, 2, 4, 1)) treearrow(from = pos[1:5, ], to = pos[6:10, ]) for (i in 1:10) textrect(pos[i, ], lab = i, cex = 2, radx = 0.05) openplotmat(main = "treearrow") pos <- coordinates(c(2, 4), hor = FALSE) treearrow(from = pos[1:2, ], to = pos[3:6, ], arr.side = 1:2, path = "V") for (i in 1:6) textrect(pos[i, ], lab = i, cex = 2, radx = 0.05) openplotmat(main = "treearrow") pos <- coordinates(c(3, 5, 7, 7, 5, 3)) treearrow(from = pos[1:15, ], to = pos[15:30, ], arr.side = 0) for (i in 1:30) textrect(pos[i, ], lab = i, cex = 1.2, radx = 0.025)openplotmat(main = "treearrow") pos <- coordinates(c(3, 2, 4, 1)) treearrow(from = pos[1:5, ], to = pos[6:10, ]) for (i in 1:10) textrect(pos[i, ], lab = i, cex = 2, radx = 0.05) openplotmat(main = "treearrow") pos <- coordinates(c(2, 4), hor = FALSE) treearrow(from = pos[1:2, ], to = pos[3:6, ], arr.side = 1:2, path = "V") for (i in 1:6) textrect(pos[i, ], lab = i, cex = 2, radx = 0.05) openplotmat(main = "treearrow") pos <- coordinates(c(3, 5, 7, 7, 5, 3)) treearrow(from = pos[1:15, ], to = pos[15:30, ], arr.side = 0) for (i in 1:30) textrect(pos[i, ], lab = i, cex = 1.2, radx = 0.025)