molNet | R Documentation |
Function to generate a molecular network object, and some basic properties of the network.
molNet(compDisMat, npcTable = NULL, cutOff = "median")
compDisMat |
Compound dissimilarity matrix, as calculated by
|
npcTable |
A data frame generated by |
cutOff |
Cut-off value for compound similarities. Any similarity
lower than this value will be set to zero when the network is generated,
which strongly affects the look of the network. The value can be set
manually to any value between 0 and 1; to the |
Molecular networks can be used to illustrate the biosynthetic/structural
similarity of phytochemical compounds in a sample, while
simultaneously visualizing their relative concentrations. molNet
creates the network, and molNetPlot
can subsequently be
used to create a plot of the network.
List with a (tbl_graph) graph object, the number of compounds,
number of NPC pathways and a measure of the modularity of the network
(see modularity
).
data(minimalCompDis)
data(minimalNPCTable)
molNet(minimalCompDis, minimalNPCTable, cutOff = 0)
data(alpinaCompDis)
molNet(compDisMat = alpinaCompDis, cutOff = 0.75)
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