XGR (version 1.1.7)

xAddCoords: Function to add coordinates into a graph according to a node attribute

Description

xAddCoords is supposed to add coordinates into a graph according to a node attribute such as community or comp.

Usage

xAddCoords(
g,
node.attr = NULL,
glayout = layout_with_kk,
edge.color.alternative = c("grey70", "grey95"),
seed = 825,
verbose = TRUE
)

Arguments

g

an object of class "igraph" (or "graphNEL") for a graph with such as a 'community' node attribute

node.attr

a charatter specifying a node attribute. If NULL or no match, it returns NULL

glayout

a graph layout function. This function can be one of "layout_nicely" (previously "layout.auto"), "layout_randomly" (previously "layout.random"), "layout_in_circle" (previously "layout.circle"), "layout_on_sphere" (previously "layout.sphere"), "layout_with_fr" (previously "layout.fruchterman.reingold"), "layout_with_kk" (previously "layout.kamada.kawai"), "layout_as_tree" (previously "layout.reingold.tilford"), "layout_with_lgl" (previously "layout.lgl"), "layout_with_graphopt" (previously "layout.graphopt"), "layout_with_sugiyama" (previously "layout.sugiyama"), "layout_with_dh" (previously "layout.davidson.harel"), "layout_with_drl" (previously "layout.drl"), "layout_with_gem" (previously "layout.gem"), "layout_with_mds", and "layout_as_bipartite". A full explanation of these layouts can be found in http://igraph.org/r/doc/layout_nicely.html

edge.color.alternative

two alternative colors for edges within the community (grey70 by default) and edges between communities (grey95 by default)

seed

an integer specifying the seed

verbose

logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

Value

It returns an igraph object, appended by node attributes including "xcoord" for x-coordinates, "ycoord" for y-coordiates, and by edge attributes including "color" for between-community edges ('grey95') and within-community edges ('grey70').

See Also

xGGnetwork

Examples

# NOT RUN {
# 1) generate a random bipartite graph
set.seed(825)
g <- sample_bipartite(100, 50, p=0.1)
V(g)$name <- V(g)

# }
# NOT RUN {
# 2) obtain and append the community
cs <- igraph::cluster_louvain(g)
set.seed(825); cs <- igraph::cluster_spinglass(g)
V(g)$community <- cs$membership
ig <- xAddCoords(g, node.attr="community",
edge.color.alternative=c("grey50","grey95"))
if(class(V(ig)$community)=='character') V(ig)$community <-
as.factor(V(ig)$community)
gp <- xGGnetwork(ig, node.label='name', node.label.size=2,
node.label.color='black', node.label.alpha=0.8, node.label.padding=0,
node.label.arrow=0, node.label.force=0.002, node.xcoord='xcoord',
node.ycoord='ycoord', node.color='community',
node.color.title='Community', colormap='jet.both', ncolors=64,
zlim=NULL,
edge.color="color",edge.color.alpha=0.5,edge.curve=0,edge.arrow.gap=0)

## make it discrete for the colorbar
gp +
scale_colour_gradientn(colors=xColormap('jet')(64),breaks=seq(1,9)) +
guides(color=guide_legend(title="Community"))

## add vertex hull for each community
df <- gp$data_nodes
ls_res <- lapply(split(x=df,f=df$community), function(z)
z[chull(z$x,z$y),])
data <- do.call(rbind, ls_res)
gp + geom_polygon(data=data, aes(x=x,y=y,group=community), alpha=0.1)
gp + geom_polygon(data=data,
aes(x=x,y=y,group=community,fill=community), alpha=0.1) +
scale_fill_gradientn(colors=xColormap('jet.both')(64)) +
guides(fill="none")
# }