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 = FALSE,
edge_width_range = c(0.1, 2),
node_size = 4,
node_color_code = NULL,
node_text_size = 6,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
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
color code for the nodes (e.g. cell labels)
size of node labels
logical. show plot
logical. return ggplot object
logical. save the plot
list of saving parameters, see showSaveParameters
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.
g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#>
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/bin/python3"
x <- cellProximityEnrichment(g, cluster_column = "leiden_clus")
cellProximityNetwork(gobject = g, CPscore = x)
#> Error in loadNamespace(x): there is no package called ‘ggraph’