# Overlay omics data onto SBGN pathway diagram

## Documentation for package ‘SBGNview’ version 1.1.0

- 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
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.