# "SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

## Documentation for package ‘SBGNview’ version 1.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

+.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