Create network from cell-cell proximity scores
cellProximityNetwork(
gobject,
CPscore,
remove_self_edges = FALSE,
self_loop_strength = 0.1,
color_depletion = "lightgreen",
color_enrichment = "red",
rescale_edge_weights = TRUE,
edge_weight_range_depletion = c(0.1, 1),
edge_weight_range_enrichment = c(1, 5),
layout = c("Fruchterman", "DrL", "Kamada-Kawai"),
only_show_enrichment_edges = F,
edge_width_range = c(0.1, 2),
node_size = 4,
node_text_size = 6,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "cellProximityNetwork"
)
giotto object
CPscore, output from cellProximityEnrichment()
remove enrichment/depletion edges with itself
size of self-loops
color for depleted cell-cell interactions
color for enriched cell-cell interactions
rescale edge weights (boolean)
numerical vector of length 2 to rescale depleted edge weights
numerical vector of length 2 to rescale enriched edge weights
layout algorithm to use to draw nodes and edges
show only the enriched pairwise scores
range of edge width
size of nodes
size of node labels
show plot
return ggplot object
directly save the plot [boolean]
list of saving parameters from all_plots_save_function
default save name for saving, don't change, change save_name in save_param
igraph plot
This function creates a network that shows the spatial proximity enrichment or depletion of cell type pairs.