Visualize cluster-cluster communication as a network graph.
Usage
plot_cluster_communication(
seurat_obj,
database_name,
clustering,
key = "total",
layout = c("circle", "spatial", "fr"),
edge_width_range = c(0.5, 3),
edge_color_by = "weight",
node_size_by = "n_cells",
node_size_range = c(5, 15),
show_self_loops = FALSE,
p_threshold = 0.05,
min_weight = NULL,
edge_color_palette = NULL,
node_color = NULL,
title = NULL
)Arguments
- seurat_obj
Seurat object with cluster communication results.
- database_name
Database name.
- clustering
Clustering name.
- key
LR pair or pathway name.
- layout
Network layout: "spatial" (uses cluster positions), "circle", "fr" (Fruchterman-Reingold).
- edge_width_range
Range for edge widths (default: c(0.5, 3)).
- edge_color_by
Color edges by: "weight", "pvalue", or fixed color.
- node_size_by
Size nodes by: "n_cells", "total_signal", or fixed.
- node_size_range
Range for node sizes (default: c(3, 10)).
- show_self_loops
Show self-communication (default: FALSE).
- p_threshold
P-value threshold for showing edges (default: 0.05).
- min_weight
Minimum edge weight to show.
- edge_color_palette
Color palette for edges.
- node_color
Color or palette for nodes.
- title
Plot title.