View source: R/spatial_interaction_visuals.R
cellProximityNetwork | R Documentation |
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 |
This function creates a network that shows the spatial proximity enrichment or depletion of cell type pairs.
igraph plot
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