multigraph: Plot and Manipulate Multigraphs in R Antonio Rivero Ostoic (@mplex)
To install multigraph with the R console, R IDE, or Notebook with R kernel in.
# 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: multiplex
Padgett's Florentine Families dataset is publicly available as a Ucinet DL file format. Use function read.dl of the multiplex package to retrieve this data.
# read the Padgett Florentine Families dataset as a Ucinet DL file
# from a public repository and storage it as an object
floflies <- multiplex::read.dl(file = "http://moreno.ss.uci.edu/padgett.dat")
# or mirror
floflies <- multiplex::read.dl(file = "http://vlado.fmf.uni-lj.si/pub/networks/data/ucinet/padgett.dat")
# adjacency matrices
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 0
Object floflies represents the Florentine families network where "PADGM" are marriage relations and "PADGB" correspond to business ties among the 16 actors.
Graph of the Florentine families network using multigraph function with the default circular layout:
Check also out the vector image of this multigraph, and note that with vector graphics the rendering may vary according to the device used.
Besides a 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 list named scp to be used in the scope argument of the 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. 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.
Some actor attributes of the Florentine Families network.
flofliesatt <- multiplex::read.dl(file = "http://moreno.ss.uci.edu/padgw.dat") # or mirror flofliesatt <- multiplex::read.dl(file = "http://vlado.fmf.uni-lj.si/pub/networks/data/ucinet/padgw.dat")
Look at flofliesatt that storages attribute 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 1
However, in order to depict the multigraph of floflies with the information contained in flofliesatt, 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 7
Now flofliesatt matches floflies for the plotting.
Redefine the scope in scp 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])
The clu argument serves to 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)
As a result, there are different ways to set the colors, and the alpha vector argument serves to set the transparency of colors in vertices, edges, and the graph background.
Support for the visualization of two-mode networks is also given by multigraph, and for the Southern Women classic dataset to illustrate some of the layout options with this package.
# read the Ucinet DL file of Davis, Gardner, Gardner Southern Women
# dataset from a public repository and storage it as an object
swomen <- multiplex::read.dl(file = "http://moreno.ss.uci.edu/davis.dat")
# or mirror
swomen <- multiplex::read.dl(file = "http://vlado.fmf.uni-lj.si/pub/networks/data/ucinet/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 0
In this case, the information can be contained in a data frame or an array as before.
Function bmgraph serves to plot two-mode data or an affiliation network as a bipartite graph.
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 dataset 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)
Function bmgraph stands for a bipartite multigraph because the actors can be affiliated by different means.
bmgraph(floflies, ecol = 1)
See Plot partially ordered semigroup
or
See Multilevel Structure of G20 Trade Network
or
Miscellaneous: Time and geographyFunction multigraph with argument "new" allows superimposing graphs over a cartographical map, for example, as with the animated plot below produced together with packages gifski and sdam that represents a network dynamic in ancient Mediterranean Sea (cf. Shipwrecks network in the Mediterranean Basin ).
# pseudo-code sdam::plot.map(type="med", new=TRUE) multigraph(net, ..., new=TRUE)
multiplex version 3 or higher.
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