multigraph: Plot and Manipulate Multigraphs in R
Author: Antonio Rivero Ostoic (@mplex)
Install multigraph
### from CRAN
install.packages("multigraph")or
### from Github
devtools::install_github("mplex/multigraph")When you load the package then multiplex is automatically invoked.
library("multigraph")
# Loading required package: multiplexMultigraph: Florentine Families data set
We work with Padgett's Florentine Families data set, which is publicly available as a Ucinet DL file format. We use function read.dl of the multiplex package to retrieve this data with the R console.
### Read the Padgett Florentine Families data set as a Ucinet DL file
### from a public repository and storage it as an object
floflies <- read.dl(file = "http://moreno.ss.uci.edu/padgett.dat")
### take a look at this data
floflies
, , PADGM
ACCIAIUOL ALBIZZI BARBADORI BISCHERI CASTELLAN GINORI GUADAGNI LAMBERTES MEDICI PAZZI PERUZZI PUCCI RIDOLFI SALVIATI STROZZI TORNABUON
ACCIAIUOL 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
ALBIZZI 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0
BARBADORI 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0
BISCHERI 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 0
CASTELLAN 0 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0
GINORI 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
GUADAGNI 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 1
LAMBERTES 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
MEDICI 1 1 1 0 0 0 0 0 0 0 0 0 1 1 0 1
PAZZI 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
PERUZZI 0 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0
PUCCI 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
RIDOLFI 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1
SALVIATI 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0
STROZZI 0 0 0 1 1 0 0 0 0 0 1 0 1 0 0 0
TORNABUON 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0
, , PADGB
ACCIAIUOL ALBIZZI BARBADORI BISCHERI CASTELLAN GINORI GUADAGNI LAMBERTES MEDICI PAZZI PERUZZI PUCCI RIDOLFI SALVIATI STROZZI TORNABUON
ACCIAIUOL 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ALBIZZI 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
BARBADORI 0 0 0 0 1 1 0 0 1 0 1 0 0 0 0 0
BISCHERI 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0
CASTELLAN 0 0 1 0 0 0 0 1 0 0 1 0 0 0 0 0
GINORI 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0
GUADAGNI 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0
LAMBERTES 0 0 0 1 1 0 1 0 0 0 1 0 0 0 0 0
MEDICI 0 0 1 0 0 1 0 0 0 1 0 0 0 1 0 1
PAZZI 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
PERUZZI 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0
PUCCI 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
RIDOLFI 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SALVIATI 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
STROZZI 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TORNABUON 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0Object floflies represents this network where "PADGM" are marriage relations, and "PADGB" correspond to business ties among 16 Florentine families.
Plotting the multigraph
We plot this network with the multigraph function:
multigraph(floflies)
The network is symmetric and the default layout of the function is circular.
Check also out the vector image of this multigraph, and note that with vectorial graphics the rendering may vary according to the device used.
Force-directed layout
Besides the circular layout, another possibility is to apply a force-directed layout for the visualization of the multiplex network. Function multigraph provides a number of arguments for graph, edges, and nodes levels, which can be recorded in an object named scp for the scope argument of this function.
# define scope of node / edge / graph characteristics as list object
scp <- list(directed = FALSE, cex = 6, fsize = 7, pos = 0, vcol = 8, ecol = 1, lwd = 2, bwd = .5)
# plot graph with customized format
multigraph(floflies, layout = "force", seed = 2, scope = scp)
# plot graph with customized format
multigraph(floflies, layout = "force", seed = 2, scope = scp, lty = 2:1, pch = 13)
Note that when the graph is depicted as undirected, then the reciprocal ties by default are collapsed. You can prevent this to happen by setting the argument collRecip to FALSE. Some arguments such as cex, lwd, lty, pch are graphical parameters of the graphics package to set the shape of both the vertices and the edges, whereas other arguments like bwd to specify the width of the bundle type, fsize for the size of the font used in node labels, or ecol and vcol for the color of respectively edges and vertices are complementary in multigraph. Moreover, by setting the pos argument to 0, the actor labels are placed in the middle of the nodes.
Multigraphs with Actor Attributes
In a similar way, we obtain some actor attributes of the Florentine Families network with the read.dl function from this repository.
flofliesatt <- read.dl(file = "http://moreno.ss.uci.edu/padgw.dat")and we take a look at the flofliesatt that storages this type of information
flofliesatt
WEALTH #PRIORS #TIES
ACCIAIUOL 10 53 2
ALBIZZI 36 65 3
RIDOLFI 27 38 4
STROZZI 146 74 29
BARBADORI 55 0 14
BISCHERI 44 12 9
CASTELLAN 20 22 18
GUADAGNI 8 21 14
LAMBERTES 42 0 14
MEDICI 103 53 54
PAZZI 48 0 7
PERUZZI 49 42 32
SALVIATI 10 35 5
TORNABUON 48 0 7
GINORI 32 0 9
PUCCI 3 0 1However, in order to depict the multigraph of floflies with the information contained in flofliesatt, we need to be sure that the order of the actors matches in both objects.
flofliesatt <- flofliesatt[order(rownames(flofliesatt)), ]
flofliesatt
WEALTH #PRIORS #TIES
ACCIAIUOL 10 53 2
ALBIZZI 36 65 3
BARBADORI 55 0 14
BISCHERI 44 12 9
CASTELLAN 20 22 18
GINORI 32 0 9
GUADAGNI 8 21 14
LAMBERTES 42 0 14
MEDICI 103 53 54
PAZZI 48 0 7
PERUZZI 49 42 32
PUCCI 3 0 1
RIDOLFI 27 38 4
SALVIATI 10 35 5
STROZZI 146 74 29
TORNABUON 48 0 7That's much better now.
The following code serves to depict this network in a way that the size of the vertices reflects the wealth of the actors.
# redefine scope of node / edge / graph characteristics
scp <- list(directed = FALSE, fsize = 8, pos = 0, lwd = 2, ecol = 1, vcol = 5)
# plot graph with customized format and actor attributes
multigraph(floflies, layout = "force", seed = 1, scope = scp, cex = flofliesatt[,1])
And with the clu argument we establish the clustering of the network with three classes of actors differentiated by the colors of the vertices.
# define scope of node / edge / graph characteristics
scp2 <- list(directed = FALSE, fsize = 8, pos = 0, lwd = 2, ecol = "white",
+ vcol = c("orange","blue","white"), clu = c(1,1,1,2,2,1,2,2,1,1,2,3,1,1,2,1), alpha = c(.5, 1, .2))
# plot graph with customized format and actor attributes
multigraph(floflies, layout = "force", seed = 1, scope = scp2, cex = flofliesatt[,1], bg = 1)
Hence, colors can be established in different ways, and the alpha vector argument serves to set the transparency of vertices, edges, and background colors respectively.
Bipartite Graph: Southern Women data set
Support for the visualization of two-mode networks is also given by multigraph and we work with the Southern Women classic data set to illustrate some of the layout options with this package.
### Read the Ucinet DL file of Davis, Gardner, Gardner Southern Women
### data set from a public repository and storage it as an object
swomen <- read.dl(file = "http://moreno.ss.uci.edu/davis.dat")
### take a look...
swomen
E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11 E12 E13 E14
EVELYN 1 1 1 1 1 1 0 1 1 0 0 0 0 0
LAURA 1 1 1 0 1 1 1 1 0 0 0 0 0 0
THERESA 0 1 1 1 1 1 1 1 1 0 0 0 0 0
BRENDA 1 0 1 1 1 1 1 1 0 0 0 0 0 0
CHARLOTTE 0 0 1 1 1 0 1 0 0 0 0 0 0 0
FRANCES 0 0 1 0 1 1 0 1 0 0 0 0 0 0
ELEANOR 0 0 0 0 1 1 1 1 0 0 0 0 0 0
PEARL 0 0 0 0 0 1 0 1 1 0 0 0 0 0
RUTH 0 0 0 0 1 0 1 1 1 0 0 0 0 0
VERNE 0 0 0 0 0 0 1 1 1 0 0 1 0 0
MYRA 0 0 0 0 0 0 0 1 1 1 0 1 0 0
KATHERINE 0 0 0 0 0 0 0 1 1 1 0 1 1 1
SYLVIA 0 0 0 0 0 0 1 1 1 1 0 1 1 1
NORA 0 0 0 0 0 1 1 0 1 1 1 1 1 1
HELEN 0 0 0 0 0 0 1 1 0 1 1 1 1 1
DOROTHY 0 0 0 0 0 0 0 1 1 1 0 1 0 0
OLIVIA 0 0 0 0 0 0 0 0 1 0 1 0 0 0
FLORA 0 0 0 0 0 0 0 0 1 0 1 0 0 0In this case the information can be contained in a data frame or an array as before.
Plotting two-mode data
Function bmgraph serves to plot two-mode data or an affiliation network as a bipartite graph.
bmgraph(swomen)
In this case actor and events have different shape by default.
Similarly to multigraph the color and shape of edges and vertices can be modified by equal arguments, and we can mirror the X axis of the plot.
# define scope of node / edge / graph characteristics as list object
scp3 <- list(cex = 3, fsize = 8, pch = c(19, 15), lwd = 1.5, vcol = 2:3, fsize = 7)
# Plot bipartite graph with customized format and horizontal reflection
bmgraph(swomen, scope = scp3, mirrorX = TRUE)
Option bip3 splits the actors in two columns, whereas bip3e will split the events.
bmgraph(swomen, layout = "bip3", scope = scp3)
Bipartite graph with clustering information of Southern Women network as in Batagelj et al, 2014 (p. 29).
# clustering of network members for permutation
clup <- list(c(8,9,7,6,1,4,2,3,5,17,18,13,16,11,10,15,14,12),
c(5,1,4,2,3,9,8,7,6,11,12,10,13,14))
# clustering of network members for layout
clunm <- list(c(rep(1,9),rep(2,9)),c(rep(1,5),rep(2,4),rep(3,5)))
# Bipartite graph with clustering
bmgraph(swomen, layout = "bipc", scope = scp3, clu = clunm, perm = clup)
The binomial projection of a two-mode data set allows obtaining a force directed layout that in this case the image is clockwise rotated 65 degrees.
bmgraph(swomen, layout = "force", seed = 1, scope = scp3, rot = 65)
Finally, function bmgraph stands for a bipartite multigraph, and this is because the actors can be affiliated at different levels.
bmgraph(floflies, ecol = 1)