layout

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Generate coordinates for plotting graphs

Some simple and not so simple functions determining the placement of the vertices for drawing a graph.

Keywords
graphs
Usage
layout.auto(graph, dim=2, ...)
layout.random(graph, params, dim=2)
layout.circle(graph, params)
layout.sphere(graph, params)
layout.fruchterman.reingold(graph, ..., dim=2, params)
layout.kamada.kawai(graph, ..., dim=2, params)
layout.spring(graph, ..., params)
layout.reingold.tilford(graph, ..., params)
layout.fruchterman.reingold.grid(graph, ..., params)
layout.lgl(graph, ..., params)
layout.graphopt(graph, ..., params=list())
layout.svd(graph, d=shortest.paths(graph), ...)
layout.norm(layout, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL,
      zmin = NULL, zmax = NULL)
Arguments
graph
The graph to place.
params
The list of function dependent parameters.
dim
Numeric constant, either 2 or 3. Some functions are able to generate 2d and 3d layouts as well, supply this argument to change the default behavior.
...
Function dependent parameters, this is an alternative notation to the params argument. For layout.auto these extra parameters are simply passed to the real layout function, if one is called.
d
The matrix used for singular value decomposition. By default it is the distance matrix of the graph.
layout
A matrix with two or three columns, the layout to normalize.
xmin,xmax
The limits for the first coordinate, if one of them or both are NULL then no normalization is performed along this direction.
ymin,ymax
The limits for the second coordinate, if one of them or both are NULL then no normalization is performed along this direction.
zmin,zmax
The limits for the third coordinate, if one of them or both are NULL then no normalization is performed along this direction.
Details

These functions calculate the coordinates of the vertices for a graph usually based on some optimality criterion.

layout.auto tries to choose an appropriate layout function for the supplied graph, and uses that to generate the layout. The current implementations works like this:

  1. If the graph has a graph attribute calledlayout, then this is used. If this attribute is an R function, then it is called, with the graph and any other extra arguments.
  2. Otherwise, if the graph has vertex attributes calledxandy, then these are used as coordinates. If the graph has an additionalzvertex attribute, that is also used.
  3. Otherwise, if the graph is connected and has less than 100 vertices, the Kamada-Kawai layout is used, by callinglayout.kamada.kawai.
  4. Otherwise, if the graph has less than 1000 vertices, then the Fruchterman-Reingold layout is used, by callinglayout.fruchterman.reingold.
  5. Otherwise the DrL layout is used,layout.drlis called.
layout.random simply places the vertices randomly on a square. It has no parameters.

layout.circle places the vertices on a unit circle equidistantly. It has no paramaters.

layout.sphere places the vertices (approximately) uniformly on the surface of a sphere, this is thus a 3d layout. It is not clear however what uniformly on a sphere means. layout.fruchterman.reingold uses a force-based algorithm proposed by Fruchterman and Reingold, see references. Parameters and their default values: [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object] This function was ported from the SNA package.

layout.kamada.kawai is another force based algorithm. Parameters and default values: [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object] This function performs very well for connected graphs, but it gives poor results for unconnected ones. This function was ported from the SNA package.

layout.spring is a spring embedder algorithm. Parameters and default values: [object Object],[object Object],[object Object],[object Object],[object Object],[object Object] This function was ported from the SNA package.

layout.reingold.tilford generates a tree-like layout, so it is mainly for trees. Parameters and default values: [object Object],[object Object],[object Object] layout.fruchterman.reingold.grid is similar to layout.fruchterman.reingold but repelling force is calculated only between vertices that are closer to each other than a limit, so it is faster. Patameters and default values: [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object] layout.lgl is for large connected graphs, it is similar to the layout generator of the Large Graph Layout software (http://bioinformatics.icmb.utexas.edu/lgl). Parameters and default values: [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

layout.graphopt is a port of the graphopt layout algorithm by Michael Schmuhl. graphopt version 0.4.1 was rewritten in C and the support for layers was removed (might be added later) and a code was a bit reorganized to avoid some unneccessary steps is the node charge (see below) is zero.

graphopt uses physical analogies for defining attracting and repelling forces among the vertices and then the physical system is simulated until it reaches an equilibrium. (There is no simulated annealing or anything like that, so a stable fixed point is not guaranteed.) See also http://www.schmuhl.org/graphopt/ for the original graphopt.

Parameters and default values: [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object] layout.svd is a currently experimental layout function based on singular value decomposition. It does not have the usual params argument, but take a single argument, the distance matrix of the graph. This function generates the layout separately for each graph component and then merges them via layout.merge.

layout.norm normalizes a layout, it linearly transforms each coordinate separately to fit into the given limits.

layout.drl is another force-driven layout generator, it is suitable for quite large graphs. See layout.drl for details.

Value

  • All these functions return a numeric matrix with at least two columns and the same number of lines as the number of vertices.

concept

Graph layout

References

Fruchterman, T.M.J. and Reingold, E.M. (1991). Graph Drawing by Force-directed Placement. Software - Practice and Experience, 21(11):1129-1164.

Kamada, T. and Kawai, S. (1989). An Algorithm for Drawing General Undirected Graphs. Information Processing Letters, 31(1):7-15.

Reingold, E and Tilford, J (1981). Tidier drawing of trees. IEEE Trans. on Softw. Eng., SE-7(2):223--228.

See Also

layout.drl, plot.igraph, tkplot

Aliases
  • layout
  • layout.auto
  • layout.random
  • layout.circle
  • layout.sphere
  • layout.fruchterman.reingold
  • layout.fruchterman.reingold.grid
  • layout.kamada.kawai
  • layout.spring
  • layout.reingold.tilford
  • layout.lgl
  • layout.svd
  • layout.graphopt
  • layout.norm
Examples
g <- graph.ring(10)
layout.random(g)
layout.kamada.kawai(g)

# Fixing ego
g <- ba.game(20, m=2)
minC <- rep(-Inf, vcount(g))
maxC <- rep(Inf, vcount(g))
minC[1] <- maxC[1] <- 0
co <- layout.fruchterman.reingold(g, minx=minC, maxx=maxC,
                                  miny=minC, maxy=maxC)
co[1,]
plot(g, layout=co, vertex.size=30, edge.arrow.size=0.2,
     vertex.label=c("ego", rep("", vcount(g)-1)), rescale=FALSE,
     xlim=range(co[,1]), ylim=range(co[,2]), vertex.label.dist=1,
     vertex.label.color="red")
axis(1)
axis(2)
Documentation reproduced from package igraph, version 0.6.5-2, License: GPL (>= 2)

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