"SBGNview: Data Analysis, Integration and Visualization on SBGN
Pathways"
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Documentation for package ‘SBGNview’ version 1.22.0
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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 matrix |
| changeIds | Change vector of input IDs to another ID type |
| downloadSbgnFile | Download pre-generated SBGN-ML file from GitHub |
| findPathways | Retrieve pathways by keywords |
| glyph-class | An object to store glyph information |
| highlightArcs | Highlight arcs by arc class |
| highlightNodes | Highlight input nodes |
| highlightPath | Highlight shortest path between two nodes |
| loadMappingTable | Generate ID mapping table from input and output ID types |
| mapped.ids | IDs mappable by SBGNview |
| outputFile | Retrieve output file information from a SBGNview object |
| outputFile<- | Set or change output file information for a SBGNview object |
| pathways.info | Information of collected pathways |
| pathways.stats | Number of pathways collected |
| print.SBGNview | Generate image files |
| renderSbgn | Overlay omics data on a SBGN pathway graph and output image files. |
| sbgn.gsets | Retrieve gene list or compound list from collected databases |
| SBGNhub.id.mapping.tables | Mapping tables available in SBGNhub |
| sbgnNodes | Extract glyph information |
| SBGNview | Overlay omics data on SBGN pathway diagram and output image files. |
| spline.arc-class | An object to store information of spline arcs |