overlap.network {NetFACS}

(Deprecated) Plots the overlap of multiple conditions as bipartite network.

Description

This function is deprecated. Please see overlap_network instead

Usage

overlap.network(
  netfacs.list,
  min.prob = 0,
  min.count = 5,
  significance = 0.01,
  specificity = 0.1,
  ignore.element = NULL,
  clusters = FALSE,
  plot.bubbles = FALSE
)

Arguments

netfacs.list

list of objects resulting from netfacs or netfacs_multiple

min.prob

minimum conditional probability that should be shown in the graph

min.count

minimum number of times that a combination should occur before being included in the graph

significance

sets the level of significance that combinations have to pass before added to the network

specificity

for the 'reduced' graph, select only elements that surpass this context specificity value

ignore.element

string vector, can be used to exclude certain elements when creating the plots

clusters

boolean; if TRUE, the cluster_fast_greedy algorithm is used to detect underlying community structure, based on the occurrence probability network

plot.bubbles

if TRUE, then the nodes in the network plots will be surrounded by bubbles; if FALSE, the edges connect the names directly