KODAMA.chem.sim {MetChem}

KODAMA chemical similarity.

Description

This function calculates the structural similarity between different metabolites and perform hierarchical clustering using the KODAMA algorithm.

Usage

KODAMA.chem.sim (smiles,
                 d=NULL,
                 k=50,
                 dissimilarity.parameters=list(),
                 kodama.matrix.parameters=list(),
                 kodama.visualization.parameters=list(),
                 hclust.parameters=list(method="ward.D"))

Arguments

smiles

A list of smile notations for the study metabolites dataset.

d

A distance structure such as that returned by dist or a full symmetric matrix containing the dissimilarities. If NULL (default), then the dissimilarity matrix will be generated by chemical.dissimilarity function. Otherwise, d will be considered as the dissimilarity matrix.

k

A number of components of multidimensional scaling.

dissimilarity.parameters

Optional parameters for chemical.dissimilarity function.

kodama.matrix.parameters

Optional parameters for KODAMA.matrix function.

kodama.visualization.parameters

Optional parameters for KODAMA.visualization function.

hclust.parameters

Optional parameters for hclust function.

Value

A list contains all results of KODAMA chemical similarity analysis and hierarchical clustering for the KODAMA dimensions.

See Also

KODAMA.matrix

Examples

data(Metabolites)

res=KODAMA.chem.sim(Metabolites$SMILES)  
plot(res$kodama$visualization)