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https://github.com/mplex/multigraph

multigraph: Plot and Manipulate Multigraphs in R
https://github.com/mplex/multigraph

bipartite-graphs bipartite-network graph graph-visualization network-analysis network-visualization plot

Last synced: 3 months ago
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multigraph: Plot and Manipulate Multigraphs in R

Host: GitHub
URL: https://github.com/mplex/multigraph
Owner: mplex
Created: 2016-08-12T13:35:47.000Z (over 8 years ago)
Default Branch: master
Last Pushed: 2024-05-14T12:25:52.000Z (6 months ago)
Last Synced: 2024-06-16T13:13:55.998Z (5 months ago)
Topics: bipartite-graphs, bipartite-network, graph, graph-visualization, network-analysis, network-visualization, plot
Language: R
Homepage: https://CRAN.R-project.org/package=multigraph
Size: 2.5 MB
Stars: 22
Watchers: 7
Forks: 1
Open Issues: 0
Metadata Files:
- Readme: README.md

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README

[![CRAN version](http://www.r-pkg.org/badges/version/multigraph)](https://cran.r-project.org/package=multigraph)
[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/grand-total/multigraph)](https://cran.rstudio.com/web/packages/multigraph/index.html)

### **`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.

```r
# from CRAN
install.packages("multigraph")
```

```r
# from Github
devtools::install_github("mplex/multigraph")
```

When you load the package then **`multiplex`** is automatically invoked.

```r
library("multigraph")
# Loading required package: multiplex
```

### Multigraph: Florentine Families dataset

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.

```r
# 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.

### Plotting multigraphs

Graph of the Florentine families network using `multigraph` function with the default circular layout:

```r
multigraph(floflies)
```
![Default layout of `multigraph`](figs/floflies.png)

Check also out the [vector image](figs/floflies.pdf) of this multigraph, and *note that with vector graphics the rendering may vary according to the device used.*

#### Force-directed layout

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.

```r
# 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)
```
![Force directed layout of `multigraph`](figs/floflies-force.png)
[vector image](figs/floflies-force.pdf)

```r
# plot graph with customized format
multigraph(floflies, layout = "force", seed = 2, scope = scp, lty = 2:1, pch = 13)
```
![Force directed layout of `multigraph` different shapes](figs/floflies-force2.png)
[vector image](figs/floflies-force2.pdf)

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.

## Multigraphs with Actor Attributes

Some actor attributes of the Florentine Families network.

```r
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

```r
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.

```r
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.

```r
# 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])
```
![Force directed layout layout of `multigraph` with attributes](figs/flofliesatt-force.png)
[vector image](figs/flofliesatt-force.pdf)

The `clu` argument serves to establish the clustering of the network with three classes of actors differentiated by the colors of the vertices.

```r
# 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)
```
![Force directed layout of `multigraph` with clustering](figs/flofliesatt-force2.png)
[vector image](figs/flofliesatt-force2.pdf)

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.

___

### Bipartite Graph: Southern Women dataset

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.

```r
# 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.

#### Plotting two-mode data

Function `bmgraph` serves to plot two-mode data or an affiliation network as a bipartite graph.

```r
bmgraph(swomen)
```
![Default layout of `bmgraph`](figs/swomen.png)
[vector image](figs/swomen.pdf)

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.

```r
# 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)
```
![Mirror X of `bmgraph`](figs/swomen2.png)
[vector image](figs/swomen2.pdf)

Option `bip3` splits the actors in two columns, whereas `bip3e` will split the events.

```r
bmgraph(swomen, layout = "bip3", scope = scp3)
```
![Mirror X of `bmgraph`](figs/swomen3.png)
[vector image](figs/swomen3.pdf)

Bipartite graph with clustering information of Southern Women network as in Batagelj et al, 2014 (p. 29).

```r
# 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)
```
![clustering `bmgraph`](figs/swomenc.png)
[vector image](figs/swomenc.pdf)

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.

```r
bmgraph(swomen, layout = "force", seed = 1, scope = scp3, rot = 65)
```
![Force directed layout of `bmgraph`](figs/swomen-force.png)
[vector image](figs/swomen-force.pdf)

Function `bmgraph` stands for a bipartite *multigraph* because the actors can be affiliated by different means.

```r
bmgraph(floflies, ecol = 1)
```
![bipartite graph of `floflies`](figs/floflies-bmgraph.png)
[vector image](figs/floflies-bmgraph.pdf)

### Cayley graph

See [Plot partially ordered semigroup](https://htmlpreview.github.io/?https://github.com/mplex/sunbelt2023/blob/main/pres/Multilevel%20Structure%20of%20G20%20Trade%20Network.html#plot-partially-ordered-semigroup)

```r
?ccgraph
```

### Multilevel graph

See [Multilevel Structure of G20 Trade Network](https://htmlpreview.github.io/?https://github.com/mplex/sunbelt2023/blob/main/pres/Multilevel%20Structure%20of%20G20%20Trade%20Network.html#multilevel-structures)

```r
?mlgraph
```

##### **Notice** for **R** (>4.0.0), use **`multiplex`** version 3 or higher.