View source: R/2LayerNet_functions.R
plexi_node_detection_2layer | R Documentation |
Detecting the nodes whose local neighbors change bweteen the two conditions.
plexi_node_detection_2layer(
embeddingSpaceList,
p.adjust.method = "none",
alpha = 0.05,
rank.prc = 0.1,
volcano.plot = TRUE,
ranksum.sort.plot = FALSE
)
embeddingSpaceList |
a list obtained by the |
p.adjust.method |
method for adjusting p-value (including methods on |
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) |
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.
the highly variable nodes
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)
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