Description Usage Arguments Value Author(s) References See Also Examples
from the list of metabolites, find and connect these metabolites through four type of relationships including biochemical reaction, enzyme catalysis, encoding gene and metabolic pathway.
1 | integrateNetwork(txtInput, organism, returnAs="json", searchBy="grinn")
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txtInput |
string containing metabolite ids. Metabolite ids are from the specified database, see |
organism |
string of species in the following format: organism = "'species'" |
returnAs |
string of output type. Specify the type of the returned network. It can be "all", "json" or "cytoscape", but default is "json". "cytoscape" is the format used in Cytoscape.js |
searchBy |
string of database name. Specify the database of which the ids used as the txtInput, see |
list of nodes and edges encapsulated in json format. Return empty list if found nothing.
Kwanjeera W kwanich@ucdavis.edu
Modify the output generation for Cytoscape.js from https://github.com/cytoscape/r-cytoscape.js/blob/master/cytoscapeJsSimpleNetwork.R
Cytoscape.js, Network library for analysis and visualisation http://js.cytoscape.org/
1 2 3 4 5 6 7 8 | # Query metabolites by PubChem ids and build a network
txtInput <- "['PubChem:3326','PubChem:3436','PubChem:7656']"
organism <- "'Homo sapiens'"
result <- integrateNetwork(txtInput, organism, returnAs="all", searchBy="PubChem")
# Query metabolites by grinn ids and build a network
txtInput <- "['C00024','C00136','C05269']"
organism <- "'Homo sapiens'"
result <- integrateNetwork(txtInput, organism, returnAs="all", searchBy="grinn")
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