visNetCircle: Function to visualise an igraph object via circle diagram

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

Description

visNetCircle is supposed to visualise a graph object of class "igraph" via circle diagram. For better visualisation, ordering of vertices is determined according to communities and degrees.

Usage

visNetCircle(
g,
com,
circles = c("single", "multiple"),
newpage = T,
ordering = NULL,
colormap = c("rainbow", "bwr", "jet", "gbr", "wyr", "br", "yr", "wb"),
vertex.label = V(g)$name,
vertex.size = log(igraph::degree(g)) + 2,
vertex.label.color = "black",
vertex.label.cex = 0.6,
vertex.label.dist = 0.75,
vertex.shape = "sphere",
edge.width = 1,
edge.lty = 1,
edge.color.within = "grey",
edge.color.crossing = "black",
mark.shape = 1,
mark.expand = 10,
...
)

Arguments

g	an object of class "igraph"
com	an object of class "communities" (see http://igraph.org/r/doc/communities.html)
circles	how circles are drawn in the plot. It can be either "single" for all communities being drawn in a single circle (by default) or "multiple" for communities being drawn in the different circles (i.e. one circle per community)
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
colormap	short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), and "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta). Alternatively, any hyphen-separated HTML color names, e.g. "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names
vertex.label	the label of the vertices. The default vertex labels are the name attribute of the nodes
vertex.size	the size of each vertex. By default, it is decided according to node degrees
vertex.label.color	the color of vertex labels
vertex.label.cex	the font size of vertex labels
vertex.label.dist	the distance of the label from the center of the vertex. If it is 0 then the label is centered on the vertex. If it is 1 then the label is displayed beside the vertex.
vertex.shape	the shape of each vertex. It can be one of "circle", "square", "csquare", "rectangle", "crectangle", "vrectangle", "pie" (http://igraph.org/r/doc/vertex.shape.pie.html), "sphere", and "none". If it sets to NULL, these vertices with negative will be "csquare" and the rest "circle".
edge.width	line width for the edges (default 1)
edge.lty	line type for the edges (default 1)
edge.color.within	the color for edges within a community (default "grey")
edge.color.crossing	the color for edges between communities (default "black")
mark.shape	a numeric scalar or vector controlling the smoothness of the vertex group marking polygons. Its possible values are between -1 (fully polygons) and 1 (fully smoothness)
mark.expand	a numeric scalar or vector, the size of the border around the marked vertex groups
...	additional graphic parameters. See http://igraph.org/r/doc/plot.common.html for the complete list.

Value

invisible

Note

none

See Also

visNet

Examples

## Not run: 
# 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")
mcolors <- palette.name(length(com))
vcolors <- mcolors[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 circle diagram
# 6a) drawn into a single circle 
visNetCircle(g=g, colormap="bwr", com=com, ordering=ordering)

# 6b) drawn into multlpe circles (one circle per community) 
visNetCircle(g=g, colormap="bwr", com=com, circles="multiple",
ordering=ordering)

# 7) as comparison, also visualise graph on 2-dimensional layout 
mark.groups <- communities(com)
mark.col <- visColoralpha(mcolors, alpha=0.2)
mark.border <- visColoralpha(mcolors, alpha=0.2)
edge.color <- c("grey", "black")[crossing(com,g)+1]
visNet(g, colormap="bwr", glayout=layout.fruchterman.reingold,
vertex.color=vcolors,
vertex.frame.color=vcolors, vertex.shape="sphere",
mark.groups=mark.groups, mark.col=mark.col,
mark.border=mark.border, mark.shape=1, mark.expand=10,
edge.color=edge.color)

## End(Not run)

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")
dev.new(): using pdf(file="Rplots2.pdf")

dnet documentation built on Feb. 20, 2020, 5:08 p.m.