plexi_node_detection_2layer {PLEXI}

Detecting the nodes whose local neighbors change bweteen the two conditions.

Description

Detecting the nodes whose local neighbors change bweteen the two conditions.

Usage

plexi_node_detection_2layer(
  embeddingSpaceList,
  p.adjust.method = "none",
  alpha = 0.05,
  rank.prc = 0.1,
  volcano.plot = TRUE,
  ranksum.sort.plot = FALSE
)

Arguments

embeddingSpaceList

a list obtained by the plexi_embedding_2layer() function.

p.adjust.method

method for adjusting p-value (including methods on p.adjust.methods). If set to "none" (default), no adjustment will be performed.

alpha

numeric value of significance level (default: 0.05)

rank.prc

numeric value of the rank percentage threshold (default: 0.1)

volcano.plot

boolean value for generating the Volcano plot (default: TRUE)

ranksum.sort.plot

boolean value for generating the sorted rank sum plot (default: FALSE)

Details

Calculating the distance of node pairs in the embedding space and check their significance. To find the significantly varying nodes in the 2-layer-network, the distance between the corresponding nodes are calculated along with the null distribution. The null distribution is obtained based on the pairwise distances on null graphs. if in plexi_embedding_2layer function null.perm=FALSE, the multiplex network does not have the two randomly permuted graphs, thus the distances between all the nodes will be used for the null distribution.

Value

the highly variable nodes

Examples

myNet = network_gen(n.nodes = 50, n.var.nodes = 5, n.var.nei = 40, noise.sd = .01)
graph_data = myNet[["data_graph"]]
embeddingSpaceList = plexi_embedding_2layer(graph.data=graph_data, train.rep=5, walk.rep=5)
Nodes = plexi_node_detection_2layer(embeddingSpaceList)