mlgraph: Multilevel graph

In mplex/multigraph: Plot and Manipulate Multigraphs

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**)

mplex/multigraph documentation built on April 14, 2024, 12:15 p.m.