visNetArc: Function to visualise an igraph object via arc diagram

In dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

Description

visNetArc is supposed to visualise a graph object of class "igraph" via arc diagram in one-dimensional layout. More precisely, it displays vertices (nodes) along an axis, with edges linked by arcs. With proper ordering of vertices (e.g. according to communities and degrees), arc diagram is able to identify clusters and bridges (as effective as two-dimensional layout). One advantage of using arc diagram is to allow for easy annotations along vertices.

Usage

visNetArc(
g,
orientation = c("vertical", "horizontal"),
newpage = T,
ordering = NULL,
labels = V(g)$name,
vertex.label.color = "black",
vertex.label.cex = 1,
vertex.color = "transparent",
vertex.frame.color = "black",
vertex.size = log(degree(g)) + 0.1,
vertex.pch = 21,
vertex.lwd = 1,
edge.color = "grey",
edge.width = 1,
edge.lty = 1,
...
)

Arguments

g	an object of class "igraph"
orientation	the orientation of the plots. It can be either "vertical" (default) or "horizontal"
newpage	logical to indicate whether to open a new page. By default, it sets to true for opening a new page
ordering	a numeric vector about the ordering of vertices. It is optional. It is highly recommend to order vertices according to communities and degrees
labels	the label of the vertices. The default vertex labels are the name attribute of the nodes
vertex.label.color	the color of vertex labels
vertex.label.cex	the font size of vertex labels
vertex.color	the fill color of the vertices. The default vertex colors are transparent
vertex.frame.color	the color of the frame of the vertices. The default vertex frame colors are black
vertex.size	the size of each vertex. By default, it is decided according to node degrees
vertex.pch	the shape of each vertex. Either an integer specifying a symbol or a single character to be used as the default in plotting points. See http://www.statmethods.net/advgraphs/parameters.html
vertex.lwd	line width for the vertices (default 1)
edge.color	the color of the edges (default "grey")
edge.width	line width for the edges (default 1)
edge.lty	line type for the edges (default 1)
...	additional graphic parameters associated with 'mtext'

Value

invisible

Note

none

See Also

visNet

Examples

# 1) generate a random graph according to the ER model
g <- erdos.renyi.game(100, 1/80)

# 2) produce the induced subgraph only based on the nodes in query
g <- dNetInduce(g, V(g), knn=0)

# 3) color nodes according to communities identified via a spin-glass model and simulated annealing
com <- spinglass.community(g, spins=4)
vgroups <- com$membership
palette.name <- visColormap(colormap="rainbow")
vcolors <- palette.name(length(com))[vgroups]

# 4) size nodes according to degrees
vdegrees <- igraph::degree(g)

# 5) sort nodes: first by communities and then degrees
tmp <- data.frame(ind=1:vcount(g), vgroups, vdegrees)
ordering <- tmp[order(vgroups,vdegrees),]$ind

# 6) visualise graph using 1-dimensional arc diagram
visNetArc(g, ordering=ordering, labels=V(g)$name,
vertex.label.color=vcolors,
vertex.color=vcolors, vertex.frame.color=vcolors,
vertex.size=log(vdegrees)+0.1)

# 7) as comparison, also visualise graph on 2-dimensional layout 
visNet(g, colormap="bwr", layout=layout.kamada.kawai(g),
vertex.label=V(g)$name,
vertex.color=vcolors, vertex.frame.color=vcolors,
vertex.shape="sphere")

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: supraHex
Loading required package: hexbin
dev.new(): using pdf(file="Rplots1.pdf")

dnet documentation built on Feb. 20, 2020, 3:01 p.m.