Package 'pathview' - Bioconductor

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24 pathviewafactortext.widthnumeric, node amplifying factor. This argument is for node size fine-tuning,its effect is subtler than expected. Only effective when kegg.native=FALSE.Default afctor=1.numeric, specifying the line width for text wrap. Only effective when kegg.native=FALSE. Default text.width=15 (characters).cpd.lab.offset numeric, specifying how much compound labels should be put above the defaultposition or node center. This argument is useful when map.cpdname=TRUE, i.e.compounds are labelled by full name, which affects the look of compound nodesand color. Only effective when kegg.native=FALSE. Default cpd.lab.offset=1.0.DetailsPathview maps and renders user data on relevant pathway graphs. Pathview is a stand alone programfor pathway based data integration and visualization. It also seamlessly integrates with pathwayand functional analysis tools for large-scale and fully automated analysis. Pathview provides strongsupport for data Integration. It works with: 1) essentially all types of biological data mappable topathways, 2) over 10 types of gene or protein IDs, and 20 types of compound or metabolite IDs, 3)pathways for over 2000 species as well as KEGG orthology, 4) varoius data attributes and formats,i.e. continuous/discrete data, matrices/vectors, single/multiple samples etc. To see mappable externalgene/protein IDs do: data(gene.idtype.list), to see mappable external compound relatedIDs do: data(rn.list); names(rn.list). Pathview generates both native KEGG view and Graphvizviews for pathways. Currently only KEGG pathways are implemented. Hopefully, pathways fromReactome, NCI and other databases will be supported in the future.ValueThe result returned by pathview function is a named list, with 2 elements ("plot.data.gene", "plot.data.cpd").Both elements are data.frame or NULL depends on the corresponding input data gene.data andcpd.data. These data.frames record the plot data for mapped gene or compound nodes: rows aremapped genes/compounds, columns are:kegg.nameslabelstypexywidthheightother columnsstandard KEGG IDs/Names for mapped nodes. It’s Entrez Gene ID or KEGGCompound Accessions.Node labels to be used when needednode type, currently 4 types are supported: "gene","enzyme", "compound" and"ortholog".x coordinate in the original KEGG pathway graph.y coordinate in the original KEGG pathway graph.node width in the original KEGG pathway graph.node height in the original KEGG pathway graph.columns of the mapped gene/compound data and corresponding pseudo-colorcodes for individual samplesThe results returned by keggview.native and codekeggview.graph are both a list of graph plottingparameters. These are not intended to be used externally.
pathview 25Author(s)Weijun Luo ReferencesLuo, W. and Brouwer, C., Pathview: an R/<strong>Bioconductor</strong> package for pathway based data integrationand visualization. Bioinformatics, 2013, 29(14): 1830-1831, doi: 10.1093/bioinformatics/btt285See Alsodownload.kegg the downloader, node.info the parser, node.map and node.color the mapper.Examples#load datadata(gse16873.d)data(demo.paths)#KEGG view: gene data onlyi
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