NEWS

Changes in vesion 2.2.6
+ Bug Fixes
   - saveSession, exportXXX -- #39 default to working directory
   - createNetworkFromDataFrame and .edgeNameToSuids -- #41 multigraph support
   - BiocCheck errors and warnings -- #42
+ Doc Fixes
   - added tests for multigraphs
Changes in vesion 2.2.5
+ Bug Fixes
   - createXXXFilter and applyFilter -- #40 network arg 
+ Doc Fixes
   - new filters vignette
Changes in vesion 2.2.4
+ Doc Fixes
   - vignettes
Changes in vesion 2.2.3
+ Doc Fixes
   - vignettes
Changes in vesion 2.2.2
+ Doc Fixes
   - new custom graphics vignette
Changes in vesion 2.2.1
+ Doc Fixes
   - vignettes, readme and test
Changes in vesion 2.2.0
+ New functions to remove duplicate edges
  - deleteDuplicateEdges
  - deleteSelfLoops
+ New node selection function
  - selectNodesConnectedBySelectedEdges
+ New visual style management functions
  - importVisualStyles
  - deleteVisualStyle
  - deleteStyleMapping
+ New edge bundling function
  - bundleEdges
+ New custom graphics options for nodes
  - setNodeCustomBarChart
  - setNodeCustomBoxChart
  - setNodeCustomHeatMapChart
  - setNodeCustomLineChart
  - setNodeCustomPieChart
  - setNodeCustomRingChart
  - setNodeCustomLinearGradient
  - setNodeCustomRadialGradient
  - setNodeCustomPosition
  - removeNodeCustomGraphics
+ New filter functions
  - applyFilter
  - createColumnFilter
  - createCompositeFilter
  - createDegreeFilter
  - getFilterList
  - exportFilters
  - importFilters
+ Improved speed on bulk node and edge property bypasses
+ Bug Fixes
  - selectEdgesConnectingSelectedNodes -- set default by.col = 'name'
  - setEdgeLineWidthMapping -- fixes input type
  - getGroupInfo -- works without collapsing first
  - getTableColumns -- work with List type columns
+ For Developers
  - Updated many functions to properly pass the base.url parameter to functions like getNetworkSuid. Please be aware and vigilent about this with future development.
  - Adopted use of seq_len(). Please be aware and vigilent.
  - Replaced all but one case of sapply() with vapply().
+ Deprecated
  - Nothing
+ Defunct
  - Previously deprecated functions in v2.0 from older 1.x version of the package

Changes in version 2.0.0
+ New converter functions between Cytoscape and iGraph
  - createIgraphFromNetwork
  - createNetworkFromIgraph
+ New converter functions between Cytoscape and R data.frames
  - createNetworkFromDataFrames
+ New converter functions between Cytoscape and Bioconductor GraphNEL
  - createNetworkFromGraph
  - createGraphFromNetwork
  - addGraphToNetwork
+ Fixed visual style "Direct" functions to set persistent bypass values
  - setNodePropertyBypass
  - setEdgePropertyBypass
  - see all setNode***Bypass and setEdge***Bypass functions
+ Streamlined interfaces to CyREST and Commands API
  - cyrestGET
  - cyrestPUT
  - cyrestPOST
  - cyrestDELETE
  - cyrestAPI
  - commandsGET
  - commandsPOST
  - commandsAPI
  - commandsHelp
+ Optional network parameter supports calls to "current" or specified Cytoscape network by name or SUID
+ New functions for importing/exporting tabular data into/out of Cytoscape
  - getTableColumns
  - loadTableData
+ New function for batch setting visual style property mappings
  - mapVisualProperty
+ Access to Cytoscape System information
  - cytoscapeVersionInfo
  - cytoscapeApiVersions
  - cytoscapeNumberOfCores
  - cytoscapeMemoryStatus
  - cytoscapeFreeMemory
+ Updated layoutCopyCat feature
+ Update network management functions
  - createSubnetwork
  - cloneNetwork
  - renameNetwork
  - importNetworkFromFile
+ Updated selection features
  - selectFirstNeighbors
  - selectEdgesConnectingSelectedNodes
  - selectEdgesAdjacentToSelectedNodes
+ New Cytoscape session functions
  - openSession
  - closeSession
+ Overhauled visual style settings to match Cytoscape's Defaults, Mappings, and Bypasses
+ Added style dependency functions, in addition to lockNodeDimensions
  - matchArrowColorToEdge
  - syncNodeCustomGraphicsSize
+ New set of functions for retrieving current visual property Values for nodes, edges and networks.
+ New functions for network-level Visual Property Defaults, Bypasses and Values.
+ Streamlined data table loading and retrieval
+ New functions for installing and managing Cytoscape Apps, e.g.,
  - installApp
  - uninstallApp
  - udpateApp
  - getInstalledApps
  - getAvailableApps
  - getAppUpdates
  - getAppStatus
+ New functions for network Collections
  - getCollectionList
  - getCollectionName
  - getCollectionSuid
  - getCollectionNetworks
+ New functions for accessing NDEx via CyNDEx2
  - importNetworkFromNDEx
  - exportNetworkToNDEx
  - updateNetworkInNDEx
  - getNetworkNDExId
+ For Developers
  - Reorganized functions into files corresponding to CyREST API, e.g., Collections, CytoscapeSystem, Layouts, Networks, etc.
+ Normalized all documentation using roxygen2
+ Streamlined interfaces to CyREST and Commands API (see above), greatly facilitating the implementation of any new functions matching CyREST or Command API additions
+ Reverted all single-instance methods to simple functions, replacing class-based signatures with simple default values
+ Established handy functions for validating network and view SUIDs
  - getNetworkName
  - getNetworkSuid
  - getNetworkViewSuid
+ Deprecated
  - Outdated function names
+ Defunct
  - CytoscapeConnection and CytoscapeWindow classes, functions and parameters