Description Usage Arguments Details Value Author(s) Examples
Ontology Network. Build gene-ontology relationship static and dynamic network.
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onto |
data.frame. Includes an 'id' column with term id (e.g. G0:0008150), a 'type' colum (e.g. BP, KEGG), a 'name' column (e.g. biological_process), a 'genes' column with string of genes of the query belonging to the ontology term (e.g. IL1RL1, IL5RA, TP53), and a 'fdr' column with FDR values. |
cutoff |
numeric. A fdr value as cutoff threshold to plot edges/nodes below cutoff |
pdf |
boolean. Saves the static network as pdf. |
html |
boolean. Saves the dynamic network as html. Applies only if dynamic=T. |
dynamic |
boolean. Produce a dynamic network. |
Layout are lgl for static network and mds for dynamic network. Read igraph and visNetwork documentation.
nodes. nodesCut. Data frames with nodes id, pval, name, and type. Cutoff applies to nodesCut.
edges. edgesCut. Data frames with edges from node, to node, and weight (p-value). Cutoff applies to edgesCut.
net. netCut. igraph object. Cutoff applies to netCut.
DynNetwork. visNetwork object and htmlwidget. Cutoff applies.
Nathan Lemonnier nathanael.lemonnier@gmail.com
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