piglet (version 1.2.0)

plotCommunityNetwork: Plot community network

Description

Creates a network visualization of allele clusters from community detection.

Usage

plotCommunityNetwork(
  x,
  layout = c("fr", "kk", "circle"),
  node_color = "cluster",
  node_size = "degree",
  edge_alpha = 0.3,
  show_labels = TRUE,
  label_size = 3,
  ...
)

Value

A ggplot object

Arguments

x

A GermlineCluster object with Leiden clustering

layout

Network layout: "fr" (Fruchterman-Reingold, default), "kk" (Kamada-Kawai), or "circle"

node_color

Variable for node color: "cluster" (default), "family", or a color value

node_size

Variable for node size: "degree" (default), "fixed", or a numeric value

edge_alpha

Alpha transparency for edges. Default is 0.3.

show_labels

Logical. Show node labels. Default is TRUE.

label_size

Size of node labels. Default is 3.

...

Additional arguments

Details

This function creates a network visualization showing:

• Nodes representing alleles, colored by cluster

• Edges weighted by sequence similarity

• Layout optimized by specified algorithm

See Also

inferAlleleClusters, detect_communities_leiden

Examples

# \donttest{
data(HVGERM)
asc <- inferAlleleClusters(HVGERM[1:30],
                           clustering_method = "leiden",
                           target_clusters = 5)
plotCommunityNetwork(asc)
# }