Package 'multigraph' reference manual

Package 'multigraph'

Title:	Plot and Manipulate Multigraphs
Description:	Functions to plot and manipulate multigraphs, signed and valued graphs, bipartite graphs, multilevel graphs, and Cayley graphs with various layout options.
Authors:	Antonio Rivero Ostoic [aut, cre]
Maintainer:	Antonio Rivero Ostoic <[email protected]>
License:	GPL-3
Version:	0.99-4
Built:	2024-09-11 04:37:04 UTC
Source:	https://github.com/mplex/multigraph

Title:

Plot and Manipulate Multigraphs

Description:

Functions to plot and manipulate multigraphs, signed and valued graphs, bipartite graphs, multilevel graphs, and Cayley graphs with various layout options.

Authors:

Antonio Rivero Ostoic [aut, cre]

Maintainer:

Antonio Rivero Ostoic <[email protected]>

License:

GPL-3

Version:

0.99-4

Built:

2024-09-11 04:37:04 UTC

Source:

https://github.com/mplex/multigraph

Help Index

Plot and Manipulate Multigraphs

Description

Functions to create and manipulate multigraphs, bipartite graphs, Cayley graphs, and valued multilevel graphs.

Details

Package:	multigraph
Type:	Package
Version:	0.99-4 (devel)
Depends:	multiplex (>= 3.0.0)
Date:	14 May 2024
License:	GPL-3

This package contains functions to plot diverse types of graphs representing complex network structures. For one-mode data, it is possible to depict signed and valued multigraphs and bipartite graphs for two-mode data as well. Moreover, multilevel graphs that combine one- and two-mode network data are represented with the latest function. Finally, Cayley graphs serve to depict relations among the ties in multiplex networks recorded in the algebraic object semigroup.

Note that this package is still under development.

Author(s)

J. Antonio Rivero Ostoic

Maintainer: Antonio Rivero Ostoic <[email protected]>

References

Ostoic, J.A.R. Algebraic Analysis of Social Networks: Models, Methods and Applications Using R, Wiley, 2021

Ostoic, J.A.R. “Algebraic Analysis of Multiple Social Networks with multiplex.” Journal of Statistical Software, 91(11), 1-41. <doi:10.18637/jss.v092.i11>

Bipartite multigraph

Description

A function to create and manipulate bipartite multigraphs

Usage

bmgraph(net, layout = c("bip", "bip3", "bip3e", "bipc", "force", "rand", "circ", 
       "stress", "CA", "circ2"), scope, coord, alpha = c(1, 1, 1), showLbs, showAtts, 
       att = NULL, lbat = "1", main = NULL, cex.main, bg, mar, directed, valued, 
       collRecip, cex, pos, lwd, lty, col, ecol, vcol, vcol0, asp, seed = NULL, 
       maxiter = 100, bwd, clu, pch, rot, mirrorX, mirrorY, mirrorV, mirrorH, hds, 
       vedist, jitter, sort, add, adc, perm, ffamily, fstyle, fsize, fcol, vclu, ...)
bmgraph(net, layout = c("bip", "bip3", "bip3e", "bipc", "force", "rand", "circ", 
       "stress", "CA", "circ2"), scope, coord, alpha = c(1, 1, 1), showLbs, showAtts, 
       att = NULL, lbat = "1", main = NULL, cex.main, bg, mar, directed, valued, 
       collRecip, cex, pos, lwd, lty, col, ecol, vcol, vcol0, asp, seed = NULL, 
       maxiter = 100, bwd, clu, pch, rot, mirrorX, mirrorY, mirrorV, mirrorH, hds, 
       vedist, jitter, sort, add, adc, perm, ffamily, fstyle, fsize, fcol, vclu, ...)

Arguments

`net`	data frame or array representing the two-mode network (see details)
`layout`	the visualization layout: `bip` (default) bipartite graph `bip3` bipartite graph with three columns `bip3e` bipartite graph with three columns for events `bipc` “clustered” bipartite graph `force` force-directed algorithm `rand` random `circ` circular `stress` stress-majorization algorithm `CA` correspondence analysis `circ2` two semi-circles
`scope`	(optional) scope of the graph (see details)
`coord`	(optional) data frame with the coordinates of the vertices; if coordinates are given then the `layout` option is ignored
`alpha`	vector (vertex, edge, `bg`) with the alpha color transparency
`showLbs`	(optional and logical) whether or not to show the vertex labels when dimnames available
`showAtts`	(optional and logical) whether or not to show the vertex attribute labels
`att`	(optional) a vector or an array representing the vertex attributes
`lbat`	(optional) labels for the vertex attributes
`main`	(optional) title of the plot
`cex.main`	(optional) size of the plot's title
`bg`	(optional) background color of the plot
`mar`	(optional) margins of the plot
`directed`	(optional and logical) whether or not the graph is directed or undirected
`valued`	(optional and logical) whether or not the graph is valued or with dichotomous data
`collRecip`	(optional and logical) whether or not collapse reciprocated edges in the undirected graph
`cex`	(optional) size of the vertices
`pos`	(optional) position of the vertices' labels (`0` means “at the center of the vertex”)
`lwd`	(optional) width of the edges; ignored if `valued` is set to `TRUE`
`lty`	(optional) shape of the edges
`col`	(optional) alias for `vcol`
`ecol`	(optional) color of the edges
`vcol`	(optional) color of the vertices
`vcol0`	(optional) color of the vertices' contour (only works for `pch 21` through `25`
`asp`	(optional) aspect ratio of the plot
`seed`	(optional) random seed number for the vertices' initial coordinates. Ignored except for `force`, `stress` and `rand`
`maxiter`	(optional) maximum number of iterations in layout algorithms. Ignored except for `force`, `stress` and `rand`
`bwd`	(optional) width of the bundle edges: ranges from `0` (edges collapsed) to the default `1` (depending on the vertices' size), and for `valued` a value greater than one is possible
`clu`	(optional) clustering of the vertices (see details)
`pch`	(optional) symbol representing the vertices
`rot`	(optional) clockwise rotation of the graph in degrees
`mirrorX`	(optional) mirror of the $X$ axis
`mirrorY`	(optional) mirror of the $Y$ axis
`mirrorV`	same as `mirrorX`
`mirrorH`	same as `mirrorY`
`hds`	(optional and experimental) arcs' head scale
`vedist`	(optional and experimental) a real number with vertex - edge distance
`jitter`	(optional) jitter in `stress` or `CA`
`sort`	(optional and logical) sort the vertex labels
`add`	(optional) add nodes to the graph's domain
`adc`	(optional) add nodes to the graph's codomain
`perm`	(optional) a list of vectors for the permutation of network members in both the domain and codomain
`ffamily`	(optional) font family
`fstyle`	(optional) font style
`fsize`	(optional) font size
`fcol`	(optional) font color
`vclu`	(optional) clustering information in both the domain and the codomain in a list of vectors with integers or `NULL` (see details)
`...`	Additional argument items (see e.g. `par`)

Details

Bipartite graphs serve as visual aids for two-mode networks. While these networks are typically represented as data frames, they can also be visualized using three-dimensional arrays, where each level corresponds to a specific type of connection, resulting in parallel edges within the bipartite graph. Additionally, a bipartite network can be generated using a force-directed algorithm to create a visual representation.

With bipartite graphs consisting of two sets of vertices, clustering information, such as vertex colors, can be stored in a list vclu with two vectors, one for each vertex set. It is possible to group all members of a vertex set into a single class by setting the corresponding vector to NULL.

Value

A plot of the two-mode network as a bipartite graph or multigraph with a projection

Author(s)

Antonio Rivero Ostoic

Examples

## two binary relations among three elements
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )

## network as bipartite graph
bmgraph(arr)

## with a force directed algorithm
bmgraph(arr, layout = "force")

## with a Correspondence Analysis method
bmgraph(arr, layout = "CA", asp = NA)

## two binary relations among three elements
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )

## network as bipartite graph
bmgraph(arr)

## with a force directed algorithm
bmgraph(arr, layout = "force")

## with a Correspondence Analysis method
bmgraph(arr, layout = "CA", asp = NA)

Cayley colour graph

Description

A function to create and manipulate bipartite Cayley colour graphs

Usage

ccgraph(x, main=NULL, seed=0, maxiter=100, alpha=c(1, 1, 1), scope, loops, 
        collRecip, undRecip, showLbs, cex.main, conc, coord, clu, cex, lwd, 
        pch, lty, bwd, bwd2, att, bg, mar, pos, asp, ecol, vcol, vcol0, lbs, 
        col, lbat, swp, swp2, scl, mirrorX, mirrorY, mirrorD, mirrorL, mirrorV, 
        mirrorH, rot, hds, vedist, ffamily, fstyle, fsize, fcol, nr, gens, ...)
ccgraph(x, main=NULL, seed=0, maxiter=100, alpha=c(1, 1, 1), scope, loops, 
        collRecip, undRecip, showLbs, cex.main, conc, coord, clu, cex, lwd, 
        pch, lty, bwd, bwd2, att, bg, mar, pos, asp, ecol, vcol, vcol0, lbs, 
        col, lbat, swp, swp2, scl, mirrorX, mirrorY, mirrorD, mirrorL, mirrorV, 
        mirrorH, rot, hds, vedist, ffamily, fstyle, fsize, fcol, nr, gens, ...)

Arguments

`x`	an algebraic structure, typically a `"Semigroup"` object class
`main`	(optional) title of the plot
`seed`	(optional) random seed number for the vertices' initial coordinates; ignored except for `force`, `stress` and `rand`
`maxiter`	(optional) maximum number of iterations in layout algorithms; ignored except for `force`, `stress` and `rand`
`alpha`	vector (vertex, edge, `bg`) with the alpha color transparency
`scope`	(optional) scope of the graph (see details)
`loops`	(optional, logical, and experimental) plot graph loops?
`collRecip`	(optional and logical) whether or not collapse reciprocated edges in the undirected graph
`undRecip`	(optional and logical) whether or not plot reciprocated edges as undirected
`showLbs`	(optional and logical) whether or not show the vertex labels when dimnames available
`cex.main`	(optional) size of the plot's title
`conc`	(optional and logical) whether the layout is concentric or not
`coord`	(optional) data frame with the coordinates of the vertices; if coordinates are given then the `layout` option is ignored
`clu`	(optional) clustering of the vertices (see details)
`cex`	(optional) size of the vertices
`lwd`	(optional) width of the edges; ignored if `valued` is set to `TRUE`
`pch`	(optional) symbol representing the vertices
`lty`	(optional) shape of the edges
`bwd`	(optional) width of the bundle edges. Ranges from `0` (edges collapsed) to the default `1` (depending on the vertices' size), and for `valued` a value greater than one is possible
`bwd2`	(optional) width of the bundle loop edges.
`att`	(optional) a vector or an array representing the vertex attributes
`bg`	(optional) background color of the plot
`mar`	(optional) margins of the plot
`pos`	(optional) position of the vertices' labels (`0` means “at the center of the vertex”)
`asp`	(optional) aspect ratio of the plot
`ecol`	(optional) color of the edges
`vcol`	(optional) color of the vertices
`vcol0`	(optional) color of the vertices' contour (only works for `pch 21` through `25`
`lbs`	(optional) vertex labels
`col`	(optional) alias for `vcol`
`lbat`	(optional) labels for the vertex attributes
`swp`	(optional and logical) whether or not to swap the bundle patterns
`swp2`	(optional and logical) whether or not to swap reciprocals
`scl`	(optional and experimental) numerical scalar ( $x$ and $y$ ) or vector ( $x$ , $y$ ) of the graph's scale
`mirrorX`	(optional) mirror of the $X$ axis
`mirrorY`	(optional) mirror of the $Y$ axis
`mirrorD`	(optional) mirror reflection across diagonal $Y=X$
`mirrorL`	(optional) mirror reflection across diagonal $Y=-X$
`mirrorV`	same as `mirrorX`
`mirrorH`	same as `mirrorY`
`rot`	(optional) clockwise rotation of the graph in degrees
`hds`	(optional and experimental) arcs' head scale
`vedist`	(optional and experimental) a real number with vertex - edge distance
`ffamily`	the font family
`fstyle`	the font style
`fsize`	the font size
`fcol`	the font color
`nr`	for `conc` layout, number of radii
`gens`	(optional when absent) semigroup generators in `x`
`...`	Additional argument items (see e.g. `par`)

Details

The Cayley colour graph is a graphical representation of the relationships among relations in the relational structure of a given multiplex network. Both nodes and directed edges represent string relations, and each shape (and color) corresponds to a specific generator relation of the semigroup structure.

Value

A plot of the semigroup or group structure.

Author(s)

Antonio Rivero Ostoic

Examples

## Create an abstract semigroup from random data
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 1 ) )

S <- semigroup(arr)

## plot semigroup's Cayley graph
ccgraph(S)
## Create an abstract semigroup from random data
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 1 ) )

S <- semigroup(arr)

## plot semigroup's Cayley graph
ccgraph(S)

Concentric layout

Description

A function to compute the graph coordinated system with a concentric layout

Usage

conc(net, nr, irot, inv, flip, mirror=c("N","X","Y","D","L"), ...)
conc(net, nr, irot, inv, flip, mirror=c("N","X","Y","D","L"), ...)

Arguments

`net`	an array representing the network relations
`nr`	a scalar with the number of radii, or a vector with the clustering of the actors.
`irot`	a scalar or vector with the “internal rotation” for each circle from closer to the center point to further away
`inv`	(optional and logical) should the circles be with an inverted ordering?
`flip`	(optional and logical) should the alternating circles be flipped?
`mirror`	mirror transformation `N` identity (default) `X` reflection through the vertical center line `Y` reflection through the horizontal center line `D` reflection across diagonal $Y=X$ `L` reflection across diagonal $Y=-X$
`...`	Additional argument items

Details

In a Euclidean plane computes the coordinated system with a concentric layout with at least two radii (unless $n = 1$ ). In case that the number of radii is not specified in nr, approx. half of the vertices are located at one radius and half in another one.

The clustering of the actors may be used to establish the location of the vertices in different radii as a numerical, character, or factor vector.

Value

A data frame with a coordinated system with two columns representing the abscissa and the ordinate in a two-dimensional rectangular Cartesian coordinate system.

Author(s)

Antonio Rivero Ostoic

Examples

## Create the data: two binary relations among three elements
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )

## Coordinates for the concentric layout with two radii
coord <- conc(arr, nr = 2)

## Plot multigraph with customized coordinates
multigraph(arr, coord = coord)

## Create the data: two binary relations among three elements
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )

## Coordinates for the concentric layout with two radii
coord <- conc(arr, nr = 2)

## Plot multigraph with customized coordinates
multigraph(arr, coord = coord)

Force directed layout

Description

A function to compute the graph coordinated system with a force directed layout algorithm

Usage

frcd(net, seed = seed, maxiter, drp, scl, mov, ...)
frcd(net, seed = seed, maxiter, drp, scl, mov, ...)

Arguments

`net`	an array representing the network relations
`seed`	(mandatory) the seed of the initial layout (see details)
`maxiter`	(optional) the maximum number of iterations
`...`	Additional argument items
`scl`	(optional and experimental) numerical scalar ( $x$ and $y$ ) or vector ( $x$ , $y$ ) of the graph's scale
`mov`	(optional and experimental) numerical scalar ( $x$ and $y$ ) or vector ( $x$ , $y$ ) to move the graph
`drp`	(optional) for `valued` networks, drop values less than specified

Details

This function is meant as an internal routine for graph visualization with a force-directed layout procedure. However, it can be used to set the coordinate system with the coord option in functions multigraph and in bmgraph. In such case, the coordinate system of the graph starts with a random displacement of nodes where NULL in the seed argument implies an initial seed based on the computer clock watch, and the number of iterations in maxiter is $60+n$ .

Value

A data frame with a coordinated system with two columns representing the abscissa and the ordinate in a two-dimensional rectangular Cartesian coordinate system.

Author(s)

Antonio Rivero Ostoic

References

Fruchterman, T.M.J., & Reingold, E.M. Graph drawing by force-directed placement. Software-Practice & Experience, 21(11), 1129-1164. 1991.

Examples

## Create the data: two binary relations among three elements
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )

## Coordinates for the force directed layout with random start
coord <- frcd(arr, seed = NULL)

## Plot multigraph with customized coordinates
multigraph(arr, coord = coord)

## Create the data: two binary relations among three elements
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )

## Coordinates for the force directed layout with random start
coord <- frcd(arr, seed = NULL)

## Plot multigraph with customized coordinates
multigraph(arr, coord = coord)

Multilevel graph

Description

A function to create and manipulate multilevel graphs

Usage

mlgraph(net, layout = c("circ", "force", "stress", "rand", "conc", "bip"), main = NULL, 
        seed = NULL, maxiter = 100, directed = TRUE, alpha = c(1, 1, 1), scope, collRecip, 
        undRecip, showLbs, showAtts, cex.main, coord, clu, cex, lwd, pch, lty, bwd, bwd2, 
        att, bg, mar, pos, asp, ecol, vcol, vcol0, col, lbat, swp, loops, swp2, mirrorX, 
        mirrorY, mirrorD, mirrorL, lbs, mirrorV, mirrorH, rot, hds, scl, vedist, ffamily, 
        fstyle, fsize, fcol, valued, modes, elv, lng, nr, ...)
mlgraph(net, layout = c("circ", "force", "stress", "rand", "conc", "bip"), main = NULL, 
        seed = NULL, maxiter = 100, directed = TRUE, alpha = c(1, 1, 1), scope, collRecip, 
        undRecip, showLbs, showAtts, cex.main, coord, clu, cex, lwd, pch, lty, bwd, bwd2, 
        att, bg, mar, pos, asp, ecol, vcol, vcol0, col, lbat, swp, loops, swp2, mirrorX, 
        mirrorY, mirrorD, mirrorL, lbs, mirrorV, mirrorH, rot, hds, scl, vedist, ffamily, 
        fstyle, fsize, fcol, valued, modes, elv, lng, nr, ...)

Arguments

`net`	a `"Multilevel"` class object or a three dimensional array with clustering information
`layout`	the visualization layout: `circ` circular `force` force-directed `stress` stress-majorization `rand` random `conc` concentric `bip` as bipartite graph
`main`	(optional) title of the plot
`seed`	(optional) random seed number for the vertices' initial coordinates. Ignored except for `force`, `stress` and `rand`
`maxiter`	(optional) maximum number of iterations in layout algorithms. Ignored except for `force`, `stress` and `rand`
`directed`	(logical) whether or not the graph is directed or undirected
`alpha`	vector (vertex, edge, `bg`) with the alpha color transparency
`scope`	(optional) scope of the graph (see details)
`collRecip`	(optional and logical) whether or not collapse reciprocated edges in the undirected graph
`undRecip`	(optional and logical) whether or not plot reciprocated edges as undirected
`showLbs`	(optional and logical) whether or not to show the vertex labels
`showAtts`	(optional and logical) whether or not to show the vertex attribute labels
`cex.main`	(optional) size of the plot's title
`coord`	(optional) data frame with the coordinates of the vertices. If coordinates are given then the `layout` option is ignored
`clu`	(optional) clustering of the vertices as a list of vectors with integers or NULL (see details)
`cex`	(optional) size of the vertices
`lwd`	(optional) width of the edges; ignored if `valued` is set to `TRUE`
`pch`	(optional) symbol representing the vertices
`lty`	(optional) shape of the edges
`bwd`	(optional) width of the bundle edges. Ranges from `0` (edges collapsed) to the default `1` (depending on the vertices' size), and for `valued` a value greater than one is possible
`bwd2`	(optional) width of the bundle loop edges.
`att`	(optional) a vector or an array representing the vertex attributes
`bg`	(optional) background color of the plot
`mar`	(optional) margins of the plot
`pos`	(optional) position of the vertices' labels (`0` means “at the center of the vertex”)
`asp`	(optional) aspect ratio of the plot
`ecol`	(optional) color of the edges
`vcol`	(optional) color of the vertices
`vcol0`	(optional) color of the vertices' contour (only works for `pch 21` through `25`
`col`	(optional) alias for `vcol`
`lbat`	(optional) labels for the vertex attributes
`swp`	(optional and logical) whether or not to swap the bundle patterns
`loops`	(optional, logical, and experimental) plot graph loops?
`swp2`	(optional and logical) whether or not to swap reciprocals
`mirrorX`	(optional) mirror of the $X$ axis
`mirrorY`	(optional) mirror of the $Y$ axis
`mirrorD`	(optional) mirror reflection across diagonal $Y=X$
`mirrorL`	(optional) mirror reflection across diagonal $Y=-X$
`lbs`	(optional) vertex labels
`mirrorV`	same as `mirrorX`
`mirrorH`	same as `mirrorY`
`rot`	(optional) clockwise rotation of the graph in degrees
`hds`	(optional and experimental) arcs' head scale
`scl`	(optional and experimental) numerical scalar ( $x$ and $y$ ) or vector ( $x$ , $y$ ) of the graph's scale
`vedist`	(optional and experimental) a real number with vertex - edge distance
`ffamily`	the font family
`fstyle`	the font style
`fsize`	the font size
`fcol`	the font color
`valued`	(optional and logical) whether the graph is depicyed as valued or not
`modes`	(optional) a vector indicating which matrices are domains and which codomains (works only with a `"Multilevel"` class object)
`elv`	(experimental) control loops 1
`lng`	(experimental) control loops 2
`nr`	integer or `NULL` with the number of radii for `conc` layout (see details)
`...`	Additional argument items (see e.g. `par`)

Details

Multilevel graphs serve to represent networks with different “levels” such as different domains in the network structure. A characteristic of multilevel networks is the existence of ties within and across domains.

Since this function can handle a large number of arguments, these can be stored as a list object that is passed through the scope option. In this case, a vector made of lists and scalars or combinations of these is accepted.

The bundle width specified by bwd and bwd2 ranges from 0 (edges collapsed) to the default 1 (depending on the vertices' size). For the valued option, a number greater than one is possible.

In a multilevel structure, argument clu is to class network members and it is possible to class all members of the domain or co-domain into a single class by setting the vector to NULL. Similarly, NULL in argument nr for the conc layout implies the use of two radii, one for each domain.

Value

A plot of the multilevel graph structure for the network

Note

Multilevel graphs depend on multilevel class objects

Author(s)

Antonio Rivero Ostoic

Examples

## Not run:
# create network data as arrays
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )
arr2 <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )

# create multilevel class object and plot multilevel graph
require(multiplex)
mlvl(arr, arr2) |> 
  mlgraph()
## End(**Not run**)
## Not run:
# create network data as arrays
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )
arr2 <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )

# create multilevel class object and plot multilevel graph
require(multiplex)
mlvl(arr, arr2) |> 
  mlgraph()
## End(**Not run**)

Multigraphs and valued multigraphs

Description

A function to create and manipulate multigraphs and valued multigraphs with different layout options

Usage

multigraph(net, layout = c("circ", "force", "stress", "conc", "rand"), scope, 
           directed=TRUE, loops, signed, valued, values, lbs, showLbs, att, lbat, 
           showAtts, main=NULL, cex.main, col.main, font.main, coord, collRecip, undRecip, 
           seed=NULL, maxiter=100, clu, cex, cex2, pch, lwd, lty, vcol, vcol0, col, ecol, 
           bwd, bwd2, pos, bg, bg2, asp, drp, add, swp, swp2, alpha=c(1, 1, 1, 1), rot, 
           mirrorX, mirrorY, mirrorD, mirrorL, mirrorV, mirrorH, scl, hds, vedist, mar, 
           ffamily, fstyle, fsize, fsize2, fcol, fcol2, lclu, sel, new, mai, lscl, 
           rm.isol, ...)
multigraph(net, layout = c("circ", "force", "stress", "conc", "rand"), scope, 
           directed=TRUE, loops, signed, valued, values, lbs, showLbs, att, lbat, 
           showAtts, main=NULL, cex.main, col.main, font.main, coord, collRecip, undRecip, 
           seed=NULL, maxiter=100, clu, cex, cex2, pch, lwd, lty, vcol, vcol0, col, ecol, 
           bwd, bwd2, pos, bg, bg2, asp, drp, add, swp, swp2, alpha=c(1, 1, 1, 1), rot, 
           mirrorX, mirrorY, mirrorD, mirrorL, mirrorV, mirrorH, scl, hds, vedist, mar, 
           ffamily, fstyle, fsize, fsize2, fcol, fcol2, lclu, sel, new, mai, lscl, 
           rm.isol, ...)

Arguments

`net`	an array; usually with three dimensions of stacked matrices where the multiple relations are placed.
`layout`	the visualization layout: `circ` circular `force` force-directed `stress` stress-majorization `conc` concentric `rand` random
`scope`	(optional) the scope of the graph (see details)
`directed`	(logical) whether or not the graph is directed or unidrected
`loops`	(optional, logical, and experimental) plot graph loops?
`signed`	(optional and logical) whether or not the graph is a signed structure
`valued`	(optional and logical) whether the graph is depicyed as valued or not
`values`	(optional and logical) print the values of the bonds in edges?
`lbs`	(optional) the vertices labels
`showLbs`	(optional and logical) whether or not show the vertex labels
`att`	(optional) a vector or an array representing the vertex attributes
`lbat`	(optional) the labels for the vertices' attributes
`showAtts`	(optional and logical) whether or not show the vertex attribute labels
`main`	(optional) title of the plot
`cex.main`	(optional) the size of the plot's title
`col.main`	(optional) the color of the plot's title
`font.main`	(optional) the font of the plot's title
`coord`	(optional) data frame with the coordinates of the vertices. If coordinates are given then the `layout` option is ignored
`collRecip`	(optional and logical) whether or not collapse reciprocated edges in the unidrected graph
`undRecip`	(optional and logical) whether or not plot reciprocated edges as undirected
`seed`	(optional) the random seed number for the vertices' initial coordinates. Ignored for `circ` and `conc`
`maxiter`	(optional) the maximum number of iterations in layout algorithms. Only for `force`, `stress`, and `rand`
`clu`	(optional) the clustering of the vertices (see details)
`cex`	(optional) the size of the vertices
`cex2`	the size of the background for the values with the `valued` option
`pch`	(optional) the symbol representing the vertices
`lwd`	(optional) the width of the edges; ignored if `valued` is set to `TRUE`
`lty`	(optional) the shape of the edges
`vcol`	(optional) the color of the vertices
`vcol0`	(optional) the color of the vertices' contour (only works for `pch 21` through `25`
`col`	(optional) alias for `vcol`
`ecol`	(optional) the color of the edges
`bwd`	(optional) the width of the bundle edges.
`bwd2`	(optional) the width of the bundle loop edges.
`pos`	(optional) the position of the vertices' labels (`0` means “in middle of vertex”)
`bg`	(optional) the background color of the plot
`bg2`	(optional) the background color for `values`
`asp`	(optional) the aspect ratio of the plot
`drp`	(optional) for `valued` networks, drop values less than the specified
`add`	(optional) nodes to add to the graph
`swp`	(optional and logical) whether or not swap the bundle patterns
`swp2`	(optional and logical) whether or not swap reciprocals
`alpha`	vector (vertex, edge, `bg`) with the alpha color transparecy
`rot`	(optional) clockwise rotation of the graph in degrees
`mirrorX`	(optional) mirror of the $X$ axis
`mirrorY`	(optional) mirror of the $Y$ axis
`mirrorD`	(optional) mirror reflection across diagonal $Y=X$
`mirrorL`	(optional) mirror reflection across diagonal $Y=-X$
`mirrorV`	same as `mirrorX`
`mirrorH`	same as `mirrorY`
`scl`	(optional and experimental) numerical scalar ( $x$ and $y$ ) or vector ( $x$ , $y$ ) of the graph's scale
`hds`	(optional and experimental) arcs' head scale
`vedist`	(optional and experimental) a real number with vertex - edge distance
`mar`	(optional) the margins of the plot
`ffamily`	the font family
`fstyle`	the font style
`fsize`	the font size
`fsize2`	the font size for `values`
`fcol`	the font color
`fcol2`	the font color for `values`
`lclu`	(optional, vector) “levels” in `clu` (see details)
`sel`	(optional, vector) selection of node's labels to plot
`new`	(optional, logical) new graph on an existing plot?
`mai`	(optional, vector) plot inner margins
`lscl`	(optional for valued graphs) loop scale
`rm.isol`	(optional) remove isolated vertices?
`...`	Additional argument items (see e.g. `par`)

Details

Multigraphs are graphs having parallel edges depicting different types of relations in a network. By default, a circular layout is applied where each type of tie has a distinctive shape and gray color scale. For better visualization, undirected multigraphs automatically collapse the reciprocal relations, and there is an argument to prevent this from happening. It is possible to combine the symbols and colors of vertices by assigning a class to each network member in the clustering option. Vertices can also have different sizes by specifying the argument with a vector with a length size similar to the network order.

The bundle width specified by bwd (and bwd2 for loops) ranges from 0 (edges collapsed) to the default 1 (depending on the vertices' size). For the valued option, numbers higher than one are possible. Use vedist to adjust vertex–edge distance for large and dense networks.

In some cases, such as when working with dynamic networks, it is needed to specify the ordering of the “levels” of the clustering information given in clu, and this is done in argument lclu.

When using new for plotting the graph with a background image, the previous plot(s), however, can require having an equivalent command to graphics::plot.new() (cf. e.g. sdam::plot.map() function).

Value

A plot of the network as a multigraph or a valued multigraph.

Author(s)

Antonio Rivero Ostoic

Examples

## Create the data: two binary relations among three elements
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )

## Plot the multigraph of this network
multigraph(arr)

## Now with a force directed algorithm
multigraph(arr, layout = "force")

## As weighted graph
multigraph(arr, weighted = TRUE)

## As signed graph
multigraph(arr, signed = TRUE)

## With loops and a costumized vertex size
multigraph(arr, cex = 3, loops = TRUE)

## Create the data: two binary relations among three elements
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )

## Plot the multigraph of this network
multigraph(arr)

## Now with a force directed algorithm
multigraph(arr, layout = "force")

## As weighted graph
multigraph(arr, weighted = TRUE)

## As signed graph
multigraph(arr, signed = TRUE)

## With loops and a costumized vertex size
multigraph(arr, cex = 3, loops = TRUE)

Stress majorization layout

Description

A function to compute the graph coordinated system with a stress majorization layout algorithm

Usage

stsm(net, seed = seed, maxiter = 40, drp, jitter, method, ...)
stsm(net, seed = seed, maxiter = 40, drp, jitter, method, ...)

Arguments

`net`	an array representing the network relations
`seed`	(mandatory) the seed of the initial layout (see details)
`maxiter`	(optional) the maximum number of iterations
`drp`	(optional) for `valued` networks, drop values less than specified
`jitter`	(optional) jitter in the layout
`method`	(optional) initial distance method (default `binary`)
`...`	Additional argument items

Details

Like the function frcd, this routine serves as an internal tool for graph visualization. It is also designed to establish the coordinate system using the coord option within the multigraph and bmgraph functions. In this scenario, the graph's coordinate system commences with nodes randomly positioned, and if NULL is entered in the seed argument, an initial seed will be generated based on the computer clock watch where the number of iterations in maxiter is $40$ .

Value

A data frame with a coordinated system with two columns representing the abscissa and the ordinate in a two-dimensional rectangular Cartesian coordinate system.

Author(s)

Antonio Rivero Ostoic

References

Gansner, E.R., Koren, Y., & North, S. Graph drawing by stress majorization. In Graph Drawing: 12th International Symposium, gd 2004, New York, NY, USA, September 29 - October 2, 2004, revised selected papers. Berlin Heidelberg: Springer. pp. 239-250. 2005.

Examples

## Create the data: two binary relations among three elements
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )

## Coordinates for the stress majorization layout with random start
coord <- stsm(arr, seed = NULL)

## Plot multigraph with customized coordinates
multigraph(arr, coord = coord)

## Create the data: two binary relations among three elements
arr <- round( replace( array(runif(18), c(3,3,2)), array(runif(18),
       c(3,3,2))>.5, 3 ) )

## Coordinates for the stress majorization layout with random start
coord <- stsm(arr, seed = NULL)

## Plot multigraph with customized coordinates
multigraph(arr, coord = coord)

Package 'multigraph'

Help Index

Plot and Manipulate Multigraphs

Description

Details

Author(s)

References

See Also

Bipartite multigraph

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Cayley colour graph

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Concentric layout

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Force directed layout

Description

Usage

Arguments

Details

Value

Author(s)

References

See Also

Examples

Multilevel graph

Description

Usage

Arguments

Details

Value

Note

Author(s)

See Also

Examples

Multigraphs and valued multigraphs

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Stress majorization layout

Description

Usage

Arguments

Details

Value

Author(s)

References

See Also

Examples