ggnet2: ggnet2 - Plot a network with ggplot2

Description Usage Arguments Details Author(s) See Also Examples

View source: R/ggnet2.R

Description

Function for plotting network objects using ggplot2, with additional control over graphical parameters that are not supported by the ggnet function. Please visit http://github.com/briatte/ggnet for the latest version of ggnet2, and https://briatte.github.io/ggnet for a vignette that contains many examples and explanations.

Usage

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ggnet2(net, mode = "fruchtermanreingold", layout.par = NULL,
  layout.exp = 0, alpha = 1, color = "grey75", shape = 19, size = 9,
  max_size = 9, na.rm = NA, palette = NULL, alpha.palette = NULL,
  alpha.legend = NA, color.palette = palette, color.legend = NA,
  shape.palette = NULL, shape.legend = NA, size.palette = NULL,
  size.legend = NA, size.zero = FALSE, size.cut = FALSE, size.min = NA,
  size.max = NA, label = FALSE, label.alpha = 1, label.color = "black",
  label.size = max_size/2, label.trim = FALSE, node.alpha = alpha,
  node.color = color, node.label = label, node.shape = shape,
  node.size = size, edge.alpha = 1, edge.color = "grey50",
  edge.lty = "solid", edge.size = 0.25, edge.label = NULL,
  edge.label.alpha = 1, edge.label.color = label.color,
  edge.label.fill = "white", edge.label.size = max_size/2, arrow.size = 0,
  arrow.gap = 0, arrow.type = "closed", legend.size = 9,
  legend.position = "right", ...)

Arguments

net

an object of class network, or any object that can be coerced to this class, such as an adjacency or incidence matrix, or an edge list: see edgeset.constructors and network for details. If the object is of class igraph and the intergraph package is installed, it will be used to convert the object: see asNetwork for details.

mode

a placement method from those provided in the sna package: see gplot.layout for details. Also accepts the names of two numeric vertex attributes of net, or a matrix of numeric coordinates, in which case the first two columns of the matrix are used. Defaults to the Fruchterman-Reingold force-directed algorithm.

layout.par

options to be passed to the placement method, as listed in gplot.layout. Defaults to NULL.

layout.exp

a multiplier to expand the horizontal axis if node labels get clipped: see expand_range for details. Defaults to 0 (no expansion).

alpha

the level of transparency of the edges and nodes, which might be a single value, a vertex attribute, or a vector of values. Also accepts "mode" on bipartite networks (see 'Details'). Defaults to 1 (no transparency).

color

the color of the nodes, which might be a single value, a vertex attribute, or a vector of values. Also accepts "mode" on bipartite networks (see 'Details'). Defaults to grey75.

shape

the shape of the nodes, which might be a single value, a vertex attribute, or a vector of values. Also accepts "mode" on bipartite networks (see 'Details'). Defaults to 19 (solid circle).

size

the size of the nodes, in points, which might be a single value, a vertex attribute, or a vector of values. Also accepts "indegree", "outdegree", "degree" or "freeman" to size the nodes by their unweighted degree centrality ("degree" and "freeman" are equivalent): see degree for details. All node sizes must be strictly positive. Also accepts "mode" on bipartite networks (see 'Details'). Defaults to 9.

max_size

the maximum size of the node when size produces nodes of different sizes, in points. Defaults to 9.

na.rm

whether to subset the network to nodes that are not missing a given vertex attribute. If set to any vertex attribute of net, the nodes for which this attribute is NA will be removed. Defaults to NA (does nothing).

palette

the palette to color the nodes, when color is not a color value or a vector of color values. Accepts named vectors of color values, or if RColorBrewer is installed, any ColorBrewer palette name: see brewer.pal and http://colorbrewer2.org/ for details. Defaults to NULL, which will create an array of grayscale color values if color is not a color value or a vector of color values.

alpha.palette

the palette to control the transparency levels of the nodes set by alpha when the levels are not numeric values. Defaults to NULL, which will create an array of alpha transparency values if alpha is not a numeric value or a vector of numeric values.

alpha.legend

the name to assign to the legend created by alpha when its levels are not numeric values. Defaults to NA (no name).

color.palette

see palette

color.legend

the name to assign to the legend created by palette. Defaults to NA (no name).

shape.palette

the palette to control the shapes of the nodes set by shape when the shapes are not numeric values. Defaults to NULL, which will create an array of shape values if shape is not a numeric value or a vector of numeric values.

shape.legend

the name to assign to the legend created by shape when its levels are not numeric values. Defaults to NA (no name).

size.palette

the palette to control the sizes of the nodes set by size when the sizes are not numeric values.

size.legend

the name to assign to the legend created by size. Defaults to NA (no name).

size.zero

whether to accept zero-sized nodes based on the value(s) of size. Defaults to FALSE, which ensures that zero-sized nodes are still shown in the plot and its size legend.

size.cut

whether to cut the size of the nodes into a certain number of quantiles. Accepts TRUE, which tries to cut the sizes into quartiles, or any positive numeric value, which tries to cut the sizes into that many quantiles. If the size of the nodes do not contain the specified number of distinct quantiles, the largest possible number is used. See quantile and cut for details. Defaults to FALSE (does nothing).

size.min

whether to subset the network to nodes with a minimum size, based on the values of size. Defaults to NA (preserves all nodes).

size.max

whether to subset the network to nodes with a maximum size, based on the values of size. Defaults to NA (preserves all nodes).

label

whether to label the nodes. If set to TRUE, nodes are labeled with their vertex names. If set to a vector that contains as many elements as there are nodes in net, nodes are labeled with these. If set to any other vector of values, the nodes are labeled only when their vertex name matches one of these values. Defaults to FALSE (no labels).

label.alpha

the level of transparency of the node labels, as a numeric value, a vector of numeric values, or as a vertex attribute containing numeric values. Defaults to 1 (no transparency).

label.color

the color of the node labels, as a color value, a vector of color values, or as a vertex attribute containing color values. Defaults to "black".

label.size

the size of the node labels, in points, as a numeric value, a vector of numeric values, or as a vertex attribute containing numeric values. Defaults to max_size / 2 (half the maximum node size), which defaults to 4.5.

label.trim

whether to apply some trimming to the node labels. Accepts any function that can process a character vector, or a strictly positive numeric value, in which case the labels are trimmed to a fixed-length substring of that length: see substr for details. Defaults to FALSE (does nothing).

node.alpha

see alpha

node.color

see color

node.label

see label

node.shape

see shape

node.size

see size

edge.alpha

the level of transparency of the edges. Defaults to the value of alpha, which defaults to 1.

edge.color

the color of the edges, as a color value, a vector of color values, or as an edge attribute containing color values. Defaults to "grey50".

edge.lty

the linetype of the edges, as a linetype value, a vector of linetype values, or as an edge attribute containing linetype values. Defaults to "solid".

edge.size

the size of the edges, in points, as a numeric value, a vector of numeric values, or as an edge attribute containing numeric values. All edge sizes must be strictly positive. Defaults to 0.25.

edge.label

the labels to plot at the middle of the edges, as a single value, a vector of values, or as an edge attribute. Defaults to NULL (no edge labels).

edge.label.alpha

the level of transparency of the edge labels, as a numeric value, a vector of numeric values, or as an edge attribute containing numeric values. Defaults to 1 (no transparency).

edge.label.color

the color of the edge labels, as a color value, a vector of color values, or as an edge attribute containing color values. Defaults to label.color, which defaults to "black".

edge.label.fill

the background color of the edge labels. Defaults to "white".

edge.label.size

the size of the edge labels, in points, as a numeric value, a vector of numeric values, or as an edge attribute containing numeric values. All edge label sizes must be strictly positive. Defaults to max_size / 2 (half the maximum node size), which defaults to 4.5.

arrow.size

the size of the arrows for directed network edges, in points. See arrow for details. Defaults to 0 (no arrows).

arrow.gap

a setting aimed at improving the display of edge arrows by plotting slightly shorter edges. Accepts any value between 0 and 1, where a value of 0.05 will generally achieve good results when the size of the nodes is reasonably small. Defaults to 0 (no shortening).

arrow.type

the type of the arrows for directed network edges. See arrow for details. Defaults to "closed".

legend.size

the size of the legend symbols and text, in points. Defaults to 9.

legend.position

the location of the plot legend(s). Accepts all legend.position values supported by theme. Defaults to "right".

...

other arguments passed to the geom_text object that sets the node labels: see geom_text for details.

Details

The degree centrality measures that can be produced through the size argument will take the directedness of the network into account, but will be unweighted. To compute weighted network measures, see the tnet package by Tore Opsahl (help("tnet", package = "tnet")).

The nodes of bipartite networks can be mapped to their mode by passing the "mode" argument to any of alpha, color, shape and size, in which case the nodes of the primary mode will be mapped as "actor", and the nodes of the secondary mode will be mapped as "event".

Author(s)

Moritz Marbach and Francois Briatte, with help from Heike Hoffmann, Pedro Jordano and Ming-Yu Liu

See Also

ggnet in this package, gplot in the sna package, and plot.network in the network package

Examples

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library(network)

# random adjacency matrix
x           <- 10
ndyads      <- x * (x - 1)
density     <- x / ndyads
m           <- matrix(0, nrow = x, ncol = x)
dimnames(m) <- list(letters[ 1:x ], letters[ 1:x ])
m[ row(m) != col(m) ] <- runif(ndyads) < density
m

# random undirected network
n <- network::network(m, directed = FALSE)
n

ggnet2(n, label = TRUE)
ggnet2(n, label = TRUE, shape = 15)
ggnet2(n, label = TRUE, shape = 15, color = "black", label.color = "white")

# add vertex attribute
x = network.vertex.names(n)
x = ifelse(x %in% c("a", "e", "i"), "vowel", "consonant")
n %v% "phono" = x

ggnet2(n, color = "phono")
ggnet2(n, color = "phono", palette = c("vowel" = "gold", "consonant" = "grey"))
ggnet2(n, shape = "phono", color = "phono")

if (require(RColorBrewer)) {

  # random groups
  n %v% "group" <- sample(LETTERS[1:3], 10, replace = TRUE)

  ggnet2(n, color = "group", palette = "Set2")

}

# random weights
n %e% "weight" <- sample(1:3, network.edgecount(n), replace = TRUE)
ggnet2(n, edge.size = "weight", edge.label = "weight")

# edge arrows on a directed network
ggnet2(network(m, directed = TRUE), arrow.gap = 0.05, arrow.size = 10)

# Padgett's Florentine wedding data
data(flo, package = "network")
flo

ggnet2(flo, label = TRUE)
ggnet2(flo, label = TRUE, label.trim = 4, vjust = -1, size = 3, color = 1)
ggnet2(flo, label = TRUE, size = 12, color = "white")

Example output

network: Classes for Relational Data
Version 1.13.0 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.

  a b c d e f g h i j
a 0 0 0 0 0 0 0 1 0 0
b 0 0 0 0 0 0 0 0 0 0
c 0 1 0 0 0 0 1 1 0 1
d 0 0 0 0 0 0 0 0 0 0
e 0 0 0 0 0 0 0 0 0 0
f 0 0 0 0 0 0 0 1 0 0
g 0 1 0 0 0 0 0 0 0 0
h 0 0 0 0 0 0 0 0 0 0
i 0 0 0 0 0 0 0 0 0 0
j 0 0 0 0 0 1 0 0 0 0
 Network attributes:
  vertices = 10 
  directed = FALSE 
  hyper = FALSE 
  loops = FALSE 
  multiple = FALSE 
  bipartite = FALSE 
  total edges= 8 
    missing edges= 0 
    non-missing edges= 8 

 Vertex attribute names: 
    vertex.names 

No edge attributes
Loading required package: sna
Loading required package: statnet.common
sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.

Loading required package: scales
Warning message:
In guide_merge.legend(init, x[[i]]) : Duplicated override.aes is ignored.
Loading required package: RColorBrewer
             Acciaiuoli Albizzi Barbadori Bischeri Castellani Ginori Guadagni
Acciaiuoli            0       0         0        0          0      0        0
Albizzi               0       0         0        0          0      1        1
Barbadori             0       0         0        0          1      0        0
Bischeri              0       0         0        0          0      0        1
Castellani            0       0         1        0          0      0        0
Ginori                0       1         0        0          0      0        0
Guadagni              0       1         0        1          0      0        0
Lamberteschi          0       0         0        0          0      0        1
Medici                1       1         1        0          0      0        0
Pazzi                 0       0         0        0          0      0        0
Peruzzi               0       0         0        1          1      0        0
Pucci                 0       0         0        0          0      0        0
Ridolfi               0       0         0        0          0      0        0
Salviati              0       0         0        0          0      0        0
Strozzi               0       0         0        1          1      0        0
Tornabuoni            0       0         0        0          0      0        1
             Lamberteschi Medici Pazzi Peruzzi Pucci Ridolfi Salviati Strozzi
Acciaiuoli              0      1     0       0     0       0        0       0
Albizzi                 0      1     0       0     0       0        0       0
Barbadori               0      1     0       0     0       0        0       0
Bischeri                0      0     0       1     0       0        0       1
Castellani              0      0     0       1     0       0        0       1
Ginori                  0      0     0       0     0       0        0       0
Guadagni                1      0     0       0     0       0        0       0
Lamberteschi            0      0     0       0     0       0        0       0
Medici                  0      0     0       0     0       1        1       0
Pazzi                   0      0     0       0     0       0        1       0
Peruzzi                 0      0     0       0     0       0        0       1
Pucci                   0      0     0       0     0       0        0       0
Ridolfi                 0      1     0       0     0       0        0       1
Salviati                0      1     1       0     0       0        0       0
Strozzi                 0      0     0       1     0       1        0       0
Tornabuoni              0      1     0       0     0       1        0       0
             Tornabuoni
Acciaiuoli            0
Albizzi               0
Barbadori             0
Bischeri              0
Castellani            0
Ginori                0
Guadagni              1
Lamberteschi          0
Medici                1
Pazzi                 0
Peruzzi               0
Pucci                 0
Ridolfi               1
Salviati              0
Strozzi               0
Tornabuoni            0

GGally documentation built on Aug. 3, 2017, 1:02 a.m.