Package 'pathview' - Bioconductor

node.map 17ReferencesLuo, W. and Brouwer, C., Pathview: an R/Bioconductor package for pathway based data integrationand visualization. Bioinformatics, 2013, 29(14): 1830-1831, doi: 10.1093/bioinformatics/btt285See Alsopathview the main function, combineKEGGnodes and reaction2edge for special treatment ofnodes or edges.Examplesxml.file=system.file("extdata", "hsa04110.xml", package = "pathview")node.data=node.info(xml.file)names(node.data)#or parse into a graph object, then extract node infogR1=pathview:::parseKGML2Graph2(xml.file, genesOnly=FALSE, expand=FALSE, split.group=FALSE)node.data=node.info(gR1)node.mapMap molecular data onto KEGG pathway nodesDescriptionThe mapper function, mapping molecular data(gene expression, metabolite abundance etc)to nodesin KEGG pathway.Usagenode.map(mol.data = NULL, node.data, node.types = c("gene", "ortholog","compound")[1], node.sum = c("sum", "mean", "median", "max", "max.abs","random")[1], entrez.gnodes=TRUE)Argumentsmol.datanode.datanode.typesEither vector (single sample) or a matrix-like data (multiple sample). Vectorshould be numeric with molecule IDs as names or it may also be character ofmolecule IDs. Character vector is treated as discrete or count data. Matrixlikedata structure has molecules as rows and samples as columns. Row namesshould be molecule IDs. Default mol.data=NULL. This argument is equivalentto gene.data or cpd.data in the pathview function. Check pahtview function formore information.a named list of 10 elements, the results returned by node.info, check the functionfor details.character, sepcify the node type to map the mol.data to, either "gene", "compound",or "compound". Default node.types="gene".