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,...

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.

Details

This package is used in R-package ecolMod, which includes many more examples.

Author(s)

Karline Soetaert (Maintainer)

See Also

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.

Examples

## 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)

Gulf of Riga autumn planktonic food web

Description

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.

Usage

Rigaweb

Format

matrix with flow values, where element ij denotes flow from compartment i to j

rownames and columnames are the components.

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

References

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.

See Also

Takapotoweb

Examples

plotweb(Rigaweb, main = "Gulf of Riga planktonic food web",
        sub = "mgC/m3/day")

Takapoto atoll planktonic food web

Description

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

Usage

Takapotoweb

Format

matrix with flow values, where element ij denotes flow from compartment i to j

rownames and columnames are the components.

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

References

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.

See Also

Rigaweb

Examples

plotweb(Takapotoweb, main = "Takapoto atoll planktonic food web",
        sub = "mgC/m2/day", lab.size = 1)

Population dynamics model transition matrix of teasel

Description

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).

Usage

Teasel

Format

matrix with transition probabilities, where element ij denotes transition from compartment j to i

rownames and columnames are the component names

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

References

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.

See Also

Rigaweb, Takapotoweb

Examples

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 2-segmented arrow between two points

Description

Connects two points with 2 segments (default = horizontal-vertical) and adds an arrowhead on (one of) the segments and at a certain distance.

Usage

bentarrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, 
          arr.side = 2, arr.pos = 0.5, path = "H", ...)

Arguments

Details

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.

Value

coordinates (x,y) where arrowhead is drawn

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

straightarrow, segmentarrow, curvedarrow, selfarrow, treearrow, splitarrow,

arrows: the comparable R function,

Arrows: more complicated arrow function from package shape.

Examples

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")

coordinates of elements on a plot

Description

estimates coordinates of elements, neatly arranged on a plot.

Usage

coordinates(pos = NULL, mx = 0.0, my = 0.0, N = length(pos), 
            hor = TRUE, relsize = 1)

Arguments

Details

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.

Value

2-columned matrix, with coordinates (x,y) of each of the elements

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

Examples

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)

adds curved arrow between two points

Description

Connects two points with an ellipsoid line and adds an arrowhead at a certain distance

Usage

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), ...)

Arguments

Details

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

Value

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

straightarrow, segmentarrow, bentarrow, selfarrow, treearrow, splitarrow,

arrows: the comparable R function,

Arrows: more complicated arrow function from package shape.

Examples

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")

electric network symbols

Description

Adds a resistor, capacitator, node, amplifier, ... to a diagrom

Usage

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(...)

Arguments

Details

Created for drawing the electrical network in the book Soetaert Karline, Jeff Cash and Francesca Mazzia. Solving differential equations in R. Springer.

Note

enResistor is synonymous for en.Resistor (to trick the builder in adding this help file to the package)

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>.

See Also

textdiamond, textellipse, textempty, texthexa, textmulti, textplain, textround

Examples

## =============================================================================
## 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 an empty plot used for diagram plotting.

Description

Creates a plotting region, bounded by [0,1] without axes, labels, titles

Usage

openplotmat (asp = NA, ...)

Arguments

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

emptyplot from package shape.

plots a graph (network), based on a transition matrix

Description

visualises a transition matrix as a number of (labeled) boxes connected by (labeled) arrows.

Usage

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, ...)

Arguments

Details

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

Value

a list containing:

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

shadowbox,

Arrowhead from package shape

try: demo(plotmat)

Examples

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

Description

plots a web, based on a flow matrix

Usage

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", ...)

Arguments

Details

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.

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

plotmat,

Rigaweb, Takapotoweb

try: demo(plotweb)

Examples

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")

adds 3-segmented arrow between two points.

Description

Connects two points with 3 segments (default = left-vertical-right) and adds an arrowhead on one of the segments at a certain distance

Usage

segmentarrow(from, to, lwd = 2, lty = 1, lcol = "black", 
             arr.col = lcol, arr.side = 2, arr.pos = 0.5, 
             path = "LVR", dd = 0.5, ...)

Arguments

Details

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.

Value

coordinates (x,y) where arrowhead is drawn

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

straightarrow, bentarrow, curvedarrow, selfarrow, treearrow, splitarrow,

arrows: the comparable R function,

Arrows: more complicated arrow function from package shape

try: demo(plotweb)

Examples

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, self-pointing arrow to a plot

Description

adds a circular arrow, from and to the same point

Usage

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, ...)

Arguments

Details

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.

Value

coordinates (x,y) where arrowhead is drawn

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

straightarrow, segmentarrow, curvedarrow, bentarrow,treearrow, splitarrow,

arrows: the comparable R function,

Arrows: more complicated arrow function from package shape.

Examples

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 a shadow to a plot

Description

adds a box, with shadow on a plot; used for writing text

Usage

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, ...)

Arguments

Details

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

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

Examples

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)

adds a branched arrow between several points

Description

connects two sets of points with a star-like structure, adds an arrowhead at a certain distance

Usage

splitarrow(from, to, lwd = 2, lty = 1, lcol = "black", arr.col = lcol, 
           arr.side = 2, arr.pos = 0.5, centre = NULL, dd = 0.5, ...)

Arguments

Details

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.

Value

coordinates (x,y) where arrowheads are drawn

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

straightarrow, segmentarrow, curvedarrow, selfarrow, bentarrow, treearrow,

arrows: the comparable R function,

Arrows: more complicated arrow function from package shape.

Examples

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)

adds straight arrow between two points

Description

Plots straight line between two points

adds an arrowhead at a certain distance.

Usage

straightarrow(from, to, lwd = 2, lty = 1, lcol = "black", 
              arr.col = lcol, arr.pos = 0.5, endhead = FALSE, 
              segment = c(0,1), ...)

Arguments

Details

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.

Value

coordinates (x,y) where arrowhead is drawn

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

bentarrow, segmentarrow, curvedarrow selfarrow, splitarrow, treearrow,

arrows: the comparable R function,

Arrows: more complicated arrow function from package shape.

Examples

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)

adds lines of text in a diamand-shaped box to a plot

Description

adds one or more lines of text, in a diamond-shaped box.

Usage

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, ...)

Arguments

Details

see shadowbox for specifications of the diamond-shaped box and its shadow.

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

textellipse, textempty,texthexa, textmulti, textplain, textrect, textround

Examples

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 lines of text in an ellipsoid box to a plot

Description

adds one or more lines of text, centered around "mid" in an ellipsoid box

Usage

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, ...)

Arguments

Details

see shadowbox for specifications of the ellipsoid-shaped box and its shadow

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

textdiamond, textempty, texthexa, textmulti, textplain, textrect, textround

Examples

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 lines of text, on a colored background to a plot

Description

adds one or more lines of text, with a colored background, no box

Usage

textempty(mid, lab = "", adj = c(0.5, 0.5), 
          box.col = "white", cex = 1, ...)

Arguments

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

textdiamond, textellipse, texthexa, textmulti, textplain, textrect, textround

Examples

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 lines of text in an hexagonal box to a plot

Description

adds one or more lines of text, centered around "mid" in an hexagonal box.

Usage

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, ...)

Arguments

Details

see shadowbox for specifications of the hexangular box and its shadow

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

textdiamond, textellipse, textempty, textmulti, textplain, textrect, textround

Examples

  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 lines of text in an multigonal box to a plot

Description

adds one or more lines of text, centered around "mid" in an multigonal box

Usage

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, ...)

Arguments

Details

see shadowbox for specifications of the multigonal box and its shadow.

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

textdiamond, textellipse, textempty, texthexa, textplain, textrect, textround.

Examples

  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 lines of text to a plot

Description

adds one or more lines of text, centered around "mid"

Usage

  textplain(mid, height = 0.1, lab = "", adj = c(0.5, 0.5), ...)

Arguments

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

textdiamond, textellipse, textempty, texthexa, textmulti, textrect, textround

Examples

  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 lines of text in a rectangular-shaped box or in a parallelogram to a plot

Description

Adds one or more lines of text, centered around "mid" in a rectangular box, or in a paralellogram

Usage

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, ...)

Arguments

Details

see shadowbox for specifications of the rectangular box and its shadow.

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

Thanks to Michael Folkes for the code of the parallelogram.

See Also

textdiamond, textellipse, textempty, texthexa, textmulti, textplain, textround

Examples

  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 lines of text in a rounded box to a plot

Description

adds one or more lines of text, centered around "mid" in an a rectangular box with rounded sides

Usage

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, ...)

Arguments

Details

see shadowbox for specifications of the box and its shadow

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

textdiamond, textellipse, textempty, texthexa, textmulti, textplain, textrect.

Examples

  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)

adds a dendrogram-like branched arrow between several points

Description

connects two sets of points with a dendrogram-like structure,

adds an arrowhead at a certain distance.

Usage

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", ...)

Arguments

Details

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.

Value

coordinates (x,y) where arrowhead is drawn

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

straightarrow, segmentarrow, curvedarrow, selfarrow, bentarrow, splitarrow,

arrows: the comparable R function,

Arrows: more complicated arrow function from package shape.

Examples

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)