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| +.SBGNview | Generic function to modify SBGN graph features |
| arc-class | An object to store arc information. |
| changeDataId | Change the data IDs of input omics data |
| changeIds | Change input IDs to another ID type |
| downloadSbgnFile | Download pre-generated SBGN-ML file from GitHub |
| findPathways | Retrieve pathways from keywords |
| getMolList | Retrieve gene list or compound list from collected databases |
| glyph-class | An object to store glyph information |
| highlightArcs | Highlight arcs by arc class |
| highlightNodes | Highlight input nodes |
| highlightPath | Given two nodes, find the shortest path between them and highlight the path. Other molecules/nodes and edges involved in reactions in the path are also highlighted. |
| loadMappingTable | Generate ID mapping table from input and output ID types. If provided a vector of input IDs (limit.to.ids argument), the function will output mapping table only containing the input IDs. Otherwise, the function will output all IDs of input and output types (restricted to a species if working on gene types and specified the "species" parameter). |
| mapped.ids | IDs mappable by SBGNview |
| outputFile | Retrieve output file information from a SBGNview object |
| outputFile<- | Set output file information for a SBGNview object |
| pathways.info | Information of collected pathways |
| pathways.stat | Number of pathways collected |
| print.SBGNview | A wrapper to run function 'renderSbgn' for all pathways in a SBGNview object and generate image files. |
| renderSbgn | Overlay omics data on a SBGN pathway graph and output image files. |
| sbgnNodes | Extract glyph information |
| SBGNview | Overlay omics data on SBGN pathway diagram and output image files. |
| SBGNview.obj | Demo SBGNview object |
| spline.arc-class | An object to store information for spline formated arcs. |