layout {igraph}R Documentation

Generate coordinates for plotting graphs

Description

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

Usage

layout.random(graph, params, dim=2)
layout.circle(graph, params)
layout.sphere(graph, params)
layout.fruchterman.reingold(graph, ..., dim=2,
      verbose=igraph.par("verbose"), params)
layout.kamada.kawai(graph, ..., dim=2,
      verbose=igraph.par("verbose"), params)
layout.spring(graph, ..., params)
layout.reingold.tilford(graph, ..., params)
layout.fruchterman.reingold.grid(graph, ...,
      verbose=igraph.par("verbose"), params)
layout.lgl(graph, ..., params)
layout.graphopt(graph, ..., verbose = igraph.par("verbose"), params = list())
layout.mds(graph, d=shortest.paths(graph), ...)
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.
verbose Logial constant, whether to show a progress bar while calculating the layout.
d The matrix used for multidimansional scaling. 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.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:

This function was ported from the SNA package.

layout.kamada.kawai is another force based algorithm. Parameters and default values:

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:

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:

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:

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:

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:

layout.mds uses metric multidimensional scaling for generating the coordinates. This function does not have the usual params argument. It can just take a single argument, the distance matrix used for multidimensional scaling. This function generates the layout separately for each graph component and then merges them via layout.merge. layout.mds is an experimental function currently.

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.

Author(s)

Gabor Csardi csardi@rmki.kfki.hu

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

Examples

g <- graph.ring(10)
layout.random(g)
layout.kamada.kawai(g)

[Package igraph version 0.5.1 Index]