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" )
| 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 |
| default_save_name | 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.