mlgraph: Multilevel graph

mlgraphR Documentation

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, ...)

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

See Also

mlvl, multigraph, bmgraph, frcd, stsm, conc

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**)

multigraph documentation built on May 29, 2024, 7:09 a.m.