Set Edge weights by group

Source: R/plotFUN.R

Use a layout which takes a weights

plotNET_groupWeight(
  g,
  groups,
  weigth.within = 100,
  weight.between = 1,
  preserve.weight.within = FALSE,
  preserve.weight.between = FALSE,
  doPlot = FALSE,
  returnOnlyWeights = TRUE
)

Arguments

g

An igraph object whose edges (get.edgelist(g)) will be re-weighted according to the membership argument.

groups

A named numeric vector with length(V(g)) integers representing each group, or, a named character vector describing each group. If names(groups)==NULL then the names of the vector will be set as names(groups) == V(g)$name. If V(g)$name==NULL, the names of the vector will be set by the Vertex index

weigth.within

The weight within a group (default = 100)

weight.between

The weight within a group (default = 1)

preserve.weight.within

If E(g)$weights is not NULL, try to preserve edge weigths within a group

preserve.weight.between

If E(g)$weights is not NULL, try to preserve edge weigths between a groups

doPlot

Plot the igraph object

returnOnlyWeights

Do not return the graph, just the weights. If FALSE this will return the graph object, otherwis it returns E(g)$weights

Value

A numeric vector with length(get.edgelist(g)) edge weights that will cluster groups defined in membership if a layout is used that can handle edge weights as a parameter (see examples).

See also

Other tools for plotting networks: plotNET_BA(), plotNET_SW(), plotNET_groupColour(), plotNET_prep()

Examples

# Make a star graph and let the odd numbers cluster together
library(igraph)
g <-make_full_graph(10, directed=FALSE)
E(g)$width <- 3
V(g)$name <- paste(1:10)
membership <- rep(c(1,2),5)
names(membership) <- V(g)$name
E(g)$weight <- plotNET_groupWeight(g,membership,1000,10)
g$layout=layout.fruchterman.reingold(g,weights=E(g)$weight)
#> Warning: `layout.fruchterman.reingold()` was deprecated in igraph 2.1.0.
#> ℹ Please use `layout_with_fr()` instead.
plot(g)


# Make 3 groups by changing the 'membership' vector
membership[3:6] <- 3
names(membership) <- V(g)$name
E(g)$weight <- plotNET_groupWeight(g,membership,1000,10)
g$layout=layout.fruchterman.reingold(g,weights=E(g)$weight)
plot(g)


# Use plotNET_groupColour for Vertex and Edge group colours
g <- plotNET_groupColour(g, membership, colourE=TRUE)

plot(g)
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to max; returning -Inf

#> Error in plot.window(...): need finite 'xlim' values