Graph {sharp}

Graph visualisation

Description

Produces an igraph object from an adjacency matrix.

Usage

Graph(
  adjacency,
  node_label = NULL,
  node_colour = NULL,
  node_shape = NULL,
  edge_colour = "grey60",
  label_colour = "grey20",
  mode = "undirected",
  weighted = FALSE,
  satellites = FALSE
)

Arguments

adjacency

adjacency matrix or output of GraphicalModel.

node_label

optional vector of node labels. This vector must contain as many entries as there are rows/columns in the adjacency matrix and must be in the same order (the order is used to assign labels to nodes).

node_colour

optional vector of node colours. This vector must contain as many entries as there are rows/columns in the adjacency matrix and must be in the same order (the order is used to assign colours to nodes). Integers, named colours or RGB values can be used.

node_shape

optional vector of node shapes. This vector must contain as many entries as there are rows/columns in the adjacency matrix and must be in the same order (the order is used to assign shapes to nodes). Possible values are "circle", "square", "triangle" or "star".

edge_colour

optional character string for edge colour. Integers, named colours or RGB values can be used.

label_colour

optional character string for label colour. Integers, named colours or RGB values can be used.

mode

character string indicating how the adjacency matrix should be interpreted. Possible values include "undirected" or "directed" (see graph_from_adjacency_matrix).

weighted

indicating if entries of the adjacency matrix should define edge width. If weighted=FALSE, an unweighted igraph object is created, all edges have the same width. If weighted=TRUE, edge width is defined by the corresponding value in the adjacency matrix. If weighted=NULL, nodes are linked by as many edges as indicated in the adjacency matrix (integer values are needed).

satellites

logical indicating if unconnected nodes (satellites) should be included in the igraph object.

Details

All functionalities implemented in igraph can be used on the output. These include cosmetic changes for the visualisation, but also various tools for network analysis (including topological properties and community detection).

The R package visNetwork offers interactive network visualisation tools. An igraph object can easily be converted to a visNetwork object (see example below).

For Cytoscape users, the RCy3 package can be used to open the network in Cytoscape.

Value

An igraph object.

See Also

Adjacency, GraphicalModel, igraph manual, visNetwork manual, Cytoscape

Examples

## From adjacency matrix

# Un-weighted
adjacency <- SimulateAdjacency(pk = 20, topology = "scale-free")
plot(Graph(adjacency))

# Weighted
adjacency <- adjacency * runif(prod(dim(adjacency)))
adjacency <- adjacency + t(adjacency)
plot(Graph(adjacency, weighted = TRUE))

# Node colours and shapes
plot(Graph(adjacency, weighted = TRUE, node_shape = "star", node_colour = "red"))


## From stability selection outputs

# Graphical model
set.seed(1)
simul <- SimulateGraphical(pk = 20)
stab <- GraphicalModel(xdata = simul$data)
plot(Graph(stab))

# Sparse PLS
if (requireNamespace("sgPLS", quietly = TRUE)) {
  set.seed(1)
  simul <- SimulateRegression(n = 50, pk = c(5, 5, 5), family = "gaussian")
  x <- simul$xdata
  y <- simul$ydata
  stab <- BiSelection(
    xdata = simul$xdata, ydata = simul$ydata,
    family = "gaussian", ncomp = 3,
    LambdaX = seq_len(ncol(x) - 1),
    implementation = SparsePLS
  )
  plot(Graph(stab))
}


## Tools from other packages

# Applying some igraph functionalities
adjacency <- SimulateAdjacency(pk = 20, topology = "scale-free")
mygraph <- Graph(adjacency)
igraph::degree(mygraph)
igraph::betweenness(mygraph)
igraph::shortest_paths(mygraph, from = 1, to = 2)
igraph::walktrap.community(mygraph)

# Interactive view using visNetwork
if (requireNamespace("visNetwork", quietly = TRUE)) {
  vgraph <- mygraph
  igraph::V(vgraph)$shape <- rep("dot", length(igraph::V(vgraph)))
  v <- visNetwork::visIgraph(vgraph)
  mylayout <- as.matrix(v$x$nodes[, c("x", "y")])
  mylayout[, 2] <- -mylayout[, 2]
  plot(mygraph, layout = mylayout)
}

# Opening in Cytoscape using RCy3
if (requireNamespace("RCy3", quietly = TRUE)) {
  # Make sure that Cytoscape is open before running the following line
  # RCy3::createNetworkFromIgraph(mygraph)
}