network: plot.network – R documentation

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plot.network

Two-Dimensional Visualization for Network Objects

Description

plot.network produces a simple two-dimensional plot of network x, using optional attribute attrname to set edge values. A variety of options are available to control vertex placement, display details, color, etc.

Usage

## S3 method for class 'network'
plot(x, ...)

## Default S3 method:
plot.network(x, attrname = NULL, 
   label = network.vertex.names(x), coord = NULL, jitter = TRUE,
   thresh = 0, usearrows = TRUE, mode = "fruchtermanreingold", 
   displayisolates = TRUE, interactive = FALSE, xlab = NULL, 
   ylab = NULL, xlim = NULL, ylim = NULL, pad = 0.2, label.pad = 0.5,
   displaylabels = !missing(label), boxed.labels = FALSE, label.pos = 0,
   label.bg = "white", vertex.sides = 50, vertex.rot = 0, vertex.lwd=1,
   arrowhead.cex = 1, label.cex = 1, loop.cex = 1, vertex.cex = 1,
   edge.col = 1, label.col = 1, vertex.col = 2, label.border = 1,
   vertex.border = 1, edge.lty = 1, label.lty = NULL, vertex.lty = 1,
   edge.lwd = 0, edge.label = NULL, edge.label.cex = 1,
   edge.label.col = 1, label.lwd = par("lwd"), edge.len = 0.5, 
   edge.curve = 0.1, edge.steps = 50, loop.steps = 20, 
   object.scale = 0.01, uselen = FALSE, usecurve = FALSE,
   suppress.axes = TRUE, vertices.last = TRUE, new = TRUE, 
   layout.par = NULL, ...)

Arguments

`x`	an object of class `network`.
`...`	additional arguments to `plot`.
`attrname`	an optional edge attribute, to be used to set edge values.
`label`	a vector of vertex labels, if desired; defaults to the vertex labels returned by `network.vertex.names`. If `label` has one element and it matches with a vertex attribute name, the value of the attribute will be used. Note that labels may be set but hidden by the `displaylabels` argument.
`coord`	user-specified vertex coordinates, in an network.size(x)x2 matrix. Where this is specified, it will override the `mode` setting.
`jitter`	boolean; should the output be jittered?
`thresh`	real number indicating the lower threshold for tie values. Only ties of value >`thresh` are displayed. By default, `thresh`=0.
`usearrows`	boolean; should arrows (rather than line segments) be used to indicate edges?
`mode`	the vertex placement algorithm; this must correspond to a `network.layout` function.
`displayisolates`	boolean; should isolates be displayed?
`interactive`	boolean; should interactive adjustment of vertex placement be attempted?
`xlab`	x axis label.
`ylab`	y axis label.
`xlim`	the x limits (min, max) of the plot.
`ylim`	the y limits of the plot.
`pad`	amount to pad the plotting range; useful if labels are being clipped.
`label.pad`	amount to pad label boxes (if `boxed.labels==TRUE`), in character size units.
`displaylabels`	boolean; should vertex labels be displayed?
`boxed.labels`	boolean; place vertex labels within boxes?
`label.pos`	position at which labels should be placed, relative to vertices. `0` results in labels which are placed away from the center of the plotting region; `1`, `2`, `3`, and `4` result in labels being placed below, to the left of, above, and to the right of vertices (respectively); and `label.pos>=5` results in labels which are plotted with no offset (i.e., at the vertex positions).
`label.bg`	background color for label boxes (if `boxed.labels==TRUE`); may be a vector, if boxes are to be of different colors.
`vertex.sides`	number of polygon sides for vertices; may be given as a vector or a vertex attribute name, if vertices are to be of different types. As of v1.12, radius of polygons are scaled so that all shapes have equal area
`vertex.rot`	angle of rotation for vertices (in degrees); may be given as a vector or a vertex attribute name, if vertices are to be rotated differently.
`vertex.lwd`	line width of vertex borders; may be given as a vector or a vertex attribute name, if vertex borders are to have different line widths.
`arrowhead.cex`	expansion factor for edge arrowheads.
`label.cex`	character expansion factor for label text.
`loop.cex`	expansion factor for loops; may be given as a vector or a vertex attribute name, if loops are to be of different sizes.
`vertex.cex`	expansion factor for vertices; may be given as a vector or a vertex attribute name, if vertices are to be of different sizes.
`edge.col`	color for edges; may be given as a vector, adjacency matrix, or edge attribute name, if edges are to be of different colors.
`label.col`	color for vertex labels; may be given as a vector or a vertex attribute name, if labels are to be of different colors.
`vertex.col`	color for vertices; may be given as a vector or a vertex attribute name, if vertices are to be of different colors.
`label.border`	label border colors (if `boxed.labels==TRUE`); may be given as a vector, if label boxes are to have different colors.
`vertex.border`	border color for vertices; may be given as a vector or a vertex attribute name, if vertex borders are to be of different colors.
`edge.lty`	line type for edge borders; may be given as a vector, adjacency matrix, or edge attribute name, if edge borders are to have different line types.
`label.lty`	line type for label boxes (if `boxed.labels==TRUE`); may be given as a vector, if label boxes are to have different line types.
`vertex.lty`	line type for vertex borders; may be given as a vector or a vertex attribute name, if vertex borders are to have different line types.
`edge.lwd`	line width scale for edges; if set greater than 0, edge widths are scaled by `edge.lwd*dat`. May be given as a vector, adjacency matrix, or edge attribute name, if edges are to have different line widths.
`edge.label`	if non-`NULL`, labels for edges will be drawn. May be given as a vector, adjacency matrix, or edge attribute name, if edges are to have different labels. A single value of `TRUE` will use edge ids as labels. NOTE: currently doesn't work for curved edges.
`edge.label.cex`	character expansion factor for edge label text; may be given as a vector or a edge attribute name, if edge labels are to have different sizes.
`edge.label.col`	color for edge labels; may be given as a vector or a edge attribute name, if labels are to be of different colors.
`label.lwd`	line width for label boxes (if `boxed.labels==TRUE`); may be given as a vector, if label boxes are to have different line widths.
`edge.len`	if `uselen==TRUE`, curved edge lengths are scaled by `edge.len`.
`edge.curve`	if `usecurve==TRUE`, the extent of edge curvature is controlled by `edge.curv`. May be given as a fixed value, vector, adjacency matrix, or edge attribute name, if edges are to have different levels of curvature.
`edge.steps`	for curved edges (excluding loops), the number of line segments to use for the curve approximation.
`loop.steps`	for loops, the number of line segments to use for the curve approximation.
`object.scale`	base length for plotting objects, as a fraction of the linear scale of the plotting region. Defaults to 0.01.
`uselen`	boolean; should we use `edge.len` to rescale edge lengths?
`usecurve`	boolean; should we use `edge.curve`?
`suppress.axes`	boolean; suppress plotting of axes?
`vertices.last`	boolean; plot vertices after plotting edges?
`new`	boolean; create a new plot? If `new==FALSE`, vertices and edges will be added to the existing plot.
`layout.par`	parameters to the `network.layout` function specified in `mode`.

Details

plot.network is the standard visualization tool for the network class. By means of clever selection of display parameters, a fair amount of display flexibility can be obtained. Vertex layout – if not specified directly using coord – is determined via one of the various available algorithms. These should be specified via the mode argument; see network.layout for a full list. User-supplied layout functions are also possible – see the aforementioned man page for details.

Note that where is.hyper(x)==TRUE, the network is converted to bipartite adjacency form prior to computing coordinates. If interactive==TRUE, then the user may modify the initial network layout by selecting an individual vertex and then clicking on the location to which this vertex is to be moved; this process may be repeated until the layout is satisfactory.

Value

A two-column matrix containing the vertex positions as x,y coordinates

Note

plot.network is adapted (with minor modifications) from the gplot function of the sna library (authors: Carter T. Butts and Alex Montgomery); eventually, these two packages will be integrated.

Author(s)

Carter T. Butts buttsc@uci.edu

References

Butts, C. T. (2008). “network: a Package for Managing Relational Data in R.” Journal of Statistical Software, 24(2). https://www.jstatsoft.org/v24/i02/

Wasserman, S., and Faust, K. (1994). Social Network Analysis: Methods and Applications. Cambridge: Cambridge University Press.

Examples

#Construct a sparse graph
m<-matrix(rbinom(100,1,1.5/9),10)
diag(m)<-0
g<-network(m)

#Plot the graph
plot(g)

#Load Padgett's marriage data
data(flo)
nflo<-network(flo)
#Display the network, indicating degree and flagging the Medicis
plot(nflo, vertex.cex=apply(flo,2,sum)+1, usearrows=FALSE,
    vertex.sides=3+apply(flo,2,sum),
    vertex.col=2+(network.vertex.names(nflo)=="Medici"))

network

Classes for Relational Data

v1.16.1

GPL (>= 2)

Authors

Carter T. Butts [aut, cre], David Hunter [ctb], Mark Handcock [ctb], Skye Bender-deMoll [ctb], Jeffrey Horner [ctb], Li Wang [ctb]

Initial release

2020-10-06