Package: KEGGgraph 1.67.0
Jitao David Zhang
KEGGgraph: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.
Authors:
KEGGgraph_1.67.0.tar.gz
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KEGGgraph.pdf |KEGGgraph.html✨
KEGGgraph/json (API)
NEWS
| # Install 'KEGGgraph' in R: |
| install.packages('KEGGgraph', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- KEGGEdgeSubtype - KEGG edge subtypes
- KEGGEdgeType - KEGG edge types
- KEGGNodeType - KEGG node types
- KEGGPATHID2NAME - KEGG pathway identifier to name
On BioConductor:KEGGgraph-1.65.0(bioc 3.20)KEGGgraph-1.64.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
pathwaysgraphandnetworkvisualizationkegg
Last updated 23 days agofrom:522a8e80c5. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | WARNING | Oct 30 2024 |
| R-4.5-linux | WARNING | Oct 30 2024 |
| R-4.4-win | WARNING | Oct 30 2024 |
| R-4.4-mac | WARNING | Oct 30 2024 |
| R-4.3-win | WARNING | Oct 30 2024 |
| R-4.3-mac | WARNING | Oct 30 2024 |
Exports:edgeDataedgesexpandKEGGPathwaygetComponentgetDisplayNamegetEntryIDgetKEGGedgeDatagetKEGGgeneLinkgetKEGGIDgetKEGGnodeDatagetKGMLurlgetNamegetNamedElementgetPathwayInfogetProductgetReactionsgetRgraphvizEdgeNamesgetSubstrategetSubtypegetTitlegetTypegetValuegraphDensityinEdgesisHomoListKEGGgraphLegendKEGGpathway2GraphKEGGpathway2reactionGraphkgmlFileName2PathwayNamemergeGraphsmergeKEGGgraphsneighborhoodnodeDatanodesnodes<-numEdgesnumNodesparseEntryparseKGMLparseKGML2DataFrameparseKGML2GraphparseKGMLexpandMapsparsePathwayInfoparseReactionparseRelationplotplotKEGGgraphpvalue2asteriskqueryKEGGsubgraphrandomSubGraphretrieveKGMLshowsplitKEGGgroupsubGraphsubGraphByNodeTypesubKEGGgraphsubtypeDisplaytranslateGeneID2KEGGIDtranslateKEGGgraphtranslateKEGGID2GeneIDugraph
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Colorectal cancer dataset | top |
| Expand KEGG node of paralogues | expandKEGGNode |
| Expand KEGG Pathway | expandKEGGPathway |
| Get a character string as label for display | getDisplayName getDisplayName,graph-method getDisplayName,KEGGNode-method getDisplayName-methods |
| Get entry ID for single or list of KEGGNode or KEGGedge object(s) | getEntryID getEntryID,KEGGEdge-method getEntryID,KEGGNode-method getEntryID,list-method getEntryID-methods |
| Get KEGG gene link | getKEGGgeneLink getKEGGgeneLink,character-method getKEGGgeneLink-methods |
| Get KEGG ID | getKEGGID getKEGGID,KEGGNode-method getKEGGID-methods |
| Get or set list of KEGG node or edge data | getKEGGedgeData getKEGGnodeData setKEGGedgeData setKEGGnodeData |
| Get KGML file (url) with KEGG PATHWAY ID and (optional) organism | getCategoryIndepKGMLurl getKGMLurl kgmlNonmetabolicName2MetabolicName retrieveKGML |
| Get 'name' attribute | getName getName,KEGGEdgeSubtype-method getName,KEGGNode-method getName,KEGGPathwayInfo-method getName-methods |
| Extract the value in a vector by name | getNamedElement |
| Get KEGG pathway info | getPathwayInfo getPathwayInfo,KEGGPathway-method getPathwayInfo-methods |
| Get KEGG reactions | getReactions getReactions,KEGGPathway-method getReactions-methods |
| Get Rgraphviz compatitable edge names | getRgraphvizEdgeNames |
| Get subtype | getSubtype getSubtype,graph-method getSubtype,KEGGEdge-method getSubtype-methods |
| Get title for given element | getTitle getTitle-methods |
| Get type attribute | getType getType,KEGGEdge-method getType,KEGGNode-method getType,KEGGReaction-method getType-methods |
| Get 'value' attribute | getValue getValue,KEGGEdgeSubtype-method getValue-methods |
| Graph density | graphDensity |
| Determines whether a list is homogenous | isHomoList |
| Class 'KEGGEdge' | entryID<-,KEGGEdge-method getName,KEGGEdge-method KEGGEdge-class show,KEGGEdge-method |
| KEGG edge subtypes | KEGGEdgeSubtype |
| Class "KEGGEdgeSubType" | getName,KEGGEdgeSubType-method getValue,KEGGEdgeSubType-method KEGGEdgeSubType-class show,KEGGEdgeSubType-method |
| KEGG edge types | KEGGEdgeType |
| class 'KEGGGraphics' | KEGGGraphics-class |
| Class "KEGGGroup" | getComponent getComponent,KEGGGroup-method KEGGGroup-class |
| Class "KEGGNode" | entryID<- entryID<-,KEGGNode-method getComponent,KEGGNode-method KEGGNode-class name<- name<-,KEGGNode-method show,KEGGNode-method |
| KEGG node types | KEGGNodeType |
| KEGG pathway identifier to name | KEGGPATHID2NAME |
| Class "KEGGPathway" | edges,KEGGPathway,ANY-method edges,KEGGPathway-method edges<- edges<-,KEGGPathway-method getName,KEGGPathway-method getTitle,KEGGPathway-method KEGGPathway-class nodes,KEGGPathway-method nodes<-,KEGGPathway,ANY-method show,KEGGPathway-method |
| Parses KEGGpathway to graph | KEGGpathway2Graph |
| Convert chemical reaction network of KEGG pathway into graph | KEGGpathway2reactionGraph |
| Class "KEGGPathwayInfo" | getTitle,KEGGPathwayInfo-method KEGGPathwayInfo-class show,KEGGPathwayInfo-method |
| Class "KEGGReaction" | getName,KEGGReaction-method getProduct getProduct,KEGGReaction-method getSubstrate getSubstrate,KEGGReaction-method KEGGReaction-class show,KEGGReaction-method |
| Convert KGML file name to pathway name | kgmlFileName2PathwayName |
| A function to merge KEGG graphs | mergeGraphs |
| Merge KEGG graphs, also merging KEGGNode and KEGGEdge attributes | mergeKEGGgraphs |
| Return the neighborhood set of given vertices | neighborhood |
| Parse ENTRY elements of KGML document | parseEntry |
| Parse 'graphics' elements in KGML files | parseGraphics |
| KGML file parser | parseKGML |
| Parse KGML file into a data frame | parseKGML2DataFrame |
| Parse KGML files into KEGG graph | parseKGML2Graph |
| A convenient function to parse KGML and expand its containing maps into one graph object | parseKGMLexpandMaps |
| Parse information of the pathway from KGML files | parsePathwayInfo |
| Parse reaction from KGML files | parseReaction |
| Parse RELATION elements from KGML files | parseRelation |
| Parse KGML relation subtype | parseSubType |
| Plot KEGG graph with Rgraphviz | KEGGgraphLegend plotKEGGgraph |
| Return common significance sign (asterisk) associated with given p value | pvalue2asterisk |
| Query the subgraph of a given KEGG graph with Entrez GeneID (s) | queryKEGGsubgraph |
| Randomly subset the given graph | randomSubGraph |
| Split KEGG group | splitKEGGgroup |
| Subset KEGG graph by node types | subGraphByNodeType |
| Subset KEGG graph, including subsetting node and edge attributes | subKEGGgraph |
| Get display information for relation subtypes | subtypeDisplay subtypeDisplay,graph-method subtypeDisplay,KEGGEdge-method subtypeDisplay,KEGGEdgeSubType-method subtypeDisplay-methods |
| Tranlate the KEGG graph from being indexed by KEGGID to another identifer | translateKEGGgraph |
| Translate between KEGGID and Entrez Gene ID | translateGeneID2KEGGID translateKEGG2GeneID translateKEGGID2GeneID |
