specmine (version 3.0.2)

pathway_analysis: Creates the metabolic pathway wanted. If any of the given compounds is present in the pathway, it is coloured differently.

Description

The pathway created contains the compounds, reactions and other paths that it connects to as nodes.

The compounds given in compounds are colored in blue, while the rest of the compounds are colored in grey.

The other paths that it may connect to are colored in orange.

Reversive reactions are colored in green and the irreversible ones in red.

Usage

pathway_analysis(compounds, pathway,
                nodeNames="kegg", nodeTooltip=FALSE,
                map.zoom=FALSE, map.layout="preset", map.width=NULL, map.height=NULL)

Arguments

compounds

Vector of compounds of interest, in kegg codes.

pathway

KEGG code (e.g., "hsa00010") of the path wanted.

nodeNames

How the nodes should be named. If "kegg", nodes are named with kegg codes. If "names", nodes are named with the common names.

nodeTooltip

If a tooltip should appear when hovering a node.

map.zoom

If the map should have the zoom in and out option.

map.layout

Layout of the map, available values are the ones of cytoscape ("breadthfirst", "preset", "cose", ...)

map.width

Width of the map, in percentage

map.height

Width of the map, in px (e.g. "500px")

Value

Shows the pathway created.

Examples

# NOT RUN {
cpds=c("HMDB0000042", "HMDB0000050", "HMDB0000452", "HMDB0001851", "HMDB0001964", "HMDB0000055",
       "HMDB0000094", "HMDB0000092", "HMDB0000174", "HMDB0000639", "HMDB0000500", "HMDB0002092",
       "HMDB0000176", "HMDB0000744", "HMDB0000223", "HMDB0000239", "HMDB0001545", "HMDB0001431",
       "HMDB0001257", "HMDB0000254", "HMDB0000254", "HMDB0000258", "HMDB0002085", "HMDB0000975",
       "HMDB0000300")
compounds=convert_hmdb_to_kegg(cpds)
##You can also convert CHEBI and SPCMNM (specmine code for metabolites) codes to KEGG
pathway_analysis(compounds, "mus00750", nodeNames="names", map.layout="preset")
# }