layout _igraph

layout __igraph

Generate coordinates for plotting graphs

1

Description

Some simple and not so simple functions determining the placement of the vertices for

drawing a graph.

2

Usage

1)

(graph, dim=2, ...)

2)

(graph, params, dim=2)

3)

(graph, params)

4)

(graph, params)

5)

ld(graph, ..., dim=2, params)

6)

(graph, ..., dim=2, params)

7)

(graph, ..., params)

8)

d(graph, ..., params)

9)

(graph, ..., params)

10)

(graph, ..., params)

11)

pt(graph, ..., params=list())

12)

(graph, d=(graph), ...)

13)

(layout, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL,

i.

zmin = NULL, zmax = NULL)

3

Arguments

graph

The graph to place.

params

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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 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.

4

Details

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

optimality criterion.

4.1

tries to choose an appropriate layout function for the supplied graph, and uses that to generate

the layout. The current implementations works like this:

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the graph has a graph attribute called ?layout?, then this is used. If this attribute is an R

function, then it is called, with the graph and any other extra arguments.

ise,

if

the

graph

has

vertex

attributes

called

?x?

and

?y?,

then

these

are

used

as

coordinates. If the graph has an additional ?z? vertex attribute, that is also used.

ise,

if

the

graph

is

connected

and

has

less

than

100

vertices,

the

Kamada-Kawai

layout is used, by calling .

ise, if the graph has less than 1000 vertices, then the Fruchterman-Reingold layout is

used, by calling ld.

ise the DrL layout is used, is called.

4.2

simply places the vertices randomly on a square. It has no parameters.

4.3

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

4.4

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.

4.5

ld

uses

a

force- based

algorithm

proposed

by

Fruchterman

and

Reingold,

see

references.

Parameters and their default values:

niter

Numeric, the number of iterations to perform (500).

coolexp

Numeric, the cooling exponent for the simulated annealing (3).

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maxdelta

aximumchange (vcount(graph)).

area

Area parameter (vcount(graph)^2).

repulserad

Cancellation radius (

area

*vcount(graph)).

weights

A vector giving edge weights or NULL. If not NULL then the attraction along the edges will be

multiplied by the given edge weights (NULL).

minx

If

not

NULL,

then

it

must

be

a

n

umeric

vector

that

gives

lower

boundaries

for

the

?x?

coordinates of the vertices. The length of the vector must match the number of vertices in the

graph.

maxx

Similar to minx, but gives the upper boundaries.

miny

Similar to minx, but gives the lower boun

daries of the ?y? coordinates.

maxy

Similar to minx, but gives the upper boundaries of the ?y? coordinates.

minz

Similar to minx, but gives the lower boundaries of the ?z? coordinates, if the dim argument is 3.

Otherwise it is ignored.

maxz

Similar to minx

, but gives the upper boundaries of the ?z? coordinates, if the dim argument is 3.

Otherwise it is ignored.

start

If given, then it should be a matrix with two columns and one line for each vertex. This matrix

will be used as starting positions for the algorithm. If not given, then a random starting matrix is

used.

This function was ported from the

SNA

package.

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4.6

is another force based algorithm. Parameters and default values:

niter

Number of iterations to perform (1000).

sigma

Sets the base standard deviation of position change proposals (vcount(graph)/4).

initemp

The initial temperature (10).

coolexp

The cooling exponent (0.99).

kkconst

Sets the Kamada- Kawai vertex attraction constant (vcount(graph)**2).

minx

If

not

NULL,

then

it

must

be

a

numeric

vector

that

gives

lower

boundaries

for

the

?x?

coordinates of the vertices. The length of the vector must match the number of vertices in the

graph.

maxx

Similar

to

minx,

but

gives

the

upper

milar

to

minx,

but

gives

the

lower

boundaries of the ?y? coordinates.

maxy

Similar to minx, but gives the upper boundaries of the ?y? coordinates.

minz

Similar to minx, but gives the lower boundaries of the ?z? coordinates, if the dim argument is 3.

Otherwise it is ignored.

maxz

Similar to

minx, but gives the upper boundaries of the ?z? coordinates, if the dim argument is 3.

Otherwise it is ignored.

start

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