Create Network from Cell-Cell Proximity Score

cellProximityNetwork()

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"
)

Arguments

gobject	giotto object
CPscore	CPscore, output from cellProximityEnrichment()
remove_self_edges	remove enrichment/depletion edges with itself
self_loop_strength	size of self-loops
color_depletion	color for depleted cell-cell interactions
color_enrichment	color for enriched cell-cell interactions
rescale_edge_weights	rescale edge weights (boolean)
edge_weight_range_depletion	numerical vector of length 2 to rescale depleted edge weights
edge_weight_range_enrichment	numerical vector of length 2 to rescale enriched edge weights
layout	layout algorithm to use to draw nodes and edges
only_show_enrichment_edges	show only the enriched pairwise scores
edge_width_range	range of edge width
node_size	size of nodes
node_text_size	size of node labels
show_plot	show plot
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters from all_plots_save_function()
default_save_name	default save name for saving, don’t change, change save_name in save_param

Value

An iGraph heatmap.

Details

This function creates a network that shows the spatial proximity enrichment or depletion of cell type pairs.