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.