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

In hfang-bristol/XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

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

# 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(is(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")

## End(Not run)

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.