NEWS

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RCy3 2.26.0

• Added documentation & checks for super-long commands - suggest users to use commandsPost() when URI too long
• Bug fixes: - check for Inf and -Inf in double columns during loadTableData, #224 - fix missing base.url in some functions
• Add test functions

RCy3 2.24.0

• Use stringi to replace uchardet
• Add test functions
• Doc fixes: - add "c" to anchor choices
• Bug fixes: - fix setNodePositionBypass to support network and base.url - use viridis color palette for continuous mapping, #210

RCy3 2.22.0

• New functions: - setNodePositionBypass - getNodeLabelPosition - setNodeLabelPositionBypass - setNodeLabelPositionDefault - getNodeLabelPositionDefault - rotateLayout - scaleLayout
• Update .verifySupportedVersions to support x.y.z
• Bug fixes: - sync node/edge_name_to_suid utility functions to include new unique_list=False parameter, #139 - getCurrentStyle and getNetworkName don't work with base.url specified, #208 - styleBypasses.lockNodeDimensions calls don't propagate base.url, #209 - no return value comes from the cytoscapePing function with the changed base.url parameter, #212

RCy3 2.20.0

• Add a delay in mergeNetworks method - Wait for Cytoscape to finish adding annotations column to Network table
• Bug fixes: - ellipsis args in createNetworkFromDataFrames, #195 - setNodeColorBypass: List of hex colors, #188

RCy3 2.18.0

• New functions: - exportPNG - exportJPG - exportPDF - exportPS - exportSVG - importFileFromUrl - selectEdgesAdjacentToNodes

RCy3 2.16.0

• Faster selectAll* functions
• Add a new vignette about cloud notebooks with RCy3
• Doc fixes: - Conflicting Brightness/Contrast documentation, #172 - Conflicting Opacity documentation, #173 - updateAnnotationText cleanup, #177
• New functions: - createView - selectAll
• Bug fixes: - addAnnotationShape customShape can only add rectangle, #160 - setEdgeLineWidthMapping issue, #164 - openAppStore function opens the Cytoscape App Store 404 web page, #169 - groupAnnotation cleanup, #175

RCy3 2.14.0

• Cleaned up dependencies, dramatically reducing RCy3 package installation time
• New functions: - add and update Annotations - uniqueList parameter added to edgeNameToEdgeSUID and nodeNameToNodeSUID, #139
• Bug fixes: - loadTableData now works with tibbles, #143 - sandboxSendTo now works with cys and png, #138 - .verifySupportedVersions fixed comparisons, #152

RCy3 2.12

• Doc fixes - note about metabolite databases, #146
• Bug fixes - createVisualStyle for notebooks, #145 - regression bug for relative paths, #141 - filepath handling in export functions, #122 - Sys.sleep added to setVisualStyle, #137

RCy3 2.12.0

• New support for cloud-hosted Jupyter notebooks! - Jyputer notebooks running RCy3 in the cloud can communicate with local Cytoscape instances - Includes a Sandbox mechanism to manage file transfers between cloud and local dir
• New functions: - addAnnotationText - getAnnotationList - deleteAnnotation - setters for Filter, Model Propagation and Catchup delays - many sandbox-related functions - getStyleMapping - getAllStyleMappings - paletteColorRandom - paletteColorBrewer* (33 in total!) - internal mapping value generators for color, opacity, dimension, line styles, arrows and shapes
• New parameters: - overwrite_file added to export functions - apply added to create_*_filter functions - ndex.url and ndex.version added to CyNDEx functions
• Consistent interchangeable handling of node|edge|network names and SUIDs
• createNetworkFromDataframes plays nice with tibbles
• Bug fixes: - .edgeNameToEdgeSUID revamped to better handle duplicate edge names

RCy3 2.10.0

• New functions: - getCurrentStyle, #15
• Added Sys.sleep to buggy CyREST steps in... - createNetworkFromDataFrames, #98 - importNetworkFromFile - importNetworkFromNDEx - exportNetworkToNDEx - updateNetworkInNDEx - importFilters - create***Filter - applyFilter - updateStyleMapping - setVisualPropertyDefault
• Refactored getNetworkViewSuid
• Handled special 404 cases in .cyError
• Bug fix #94: added base.url param
• Overhauled error handling and messaging

RCy3 2.8.0

• New functions: - mergeNetworks - analyzeNetwork
• Better messaging for... - App-related functions, like installApp - When style changes are applied to "default" style

RCy3 2.6

• Doc Fixes - Roxygen update and man pages - Fixes to unitTests
• Bug Fixes - getSelectedNodes/Edges -- #82 fixed missing param in usage - added missing base.url args -- #88

RCy3 2.6.0

• New functions: - createGroupByColumn - clearEdgeBends - getNodePosition
• New parameter to return SUIDs for - getSelectedNodes - getSelectedEdges
• Node and edge property values returned as named lists
• Faster results for getting all node and edge property values, #78
• More robust handling of file type in export functions
• More robust handling of dataframes in createNetworkFromDataFrames
• New support for loading list data
• Doc Fixes - added Filters to Overview vignette - improved file type handling descriptions

RCy3 2.4.4

• Bug Fixes - filter functions -- #73 wrong params

RCy3 2.4.3

• Bug Fixes - import functions -- #62 fixed default directory

RCy3 2.4.2

• Bug Fixes - getEdgeInfo -- #61 missing function

RCy3 2.4.1

• Bug Fixes - getLayoutPropertyNames -- #59 fixed returned values - createNetworkFromIgraph -- #58 flatten list attributes to strings

RCy3 2.4.0

• New style setting functions - setEdgeFontFaceDefault - setEdgeFontFaceMapping - setEdgeFontSizeMapping - setEdgeLabelDefault - setEdgeLabelColorDefault - setEdgeLabelColorMapping - setEdgeLabelOpacityDefault - setEdgeLabelOpacityMapping - setEdgeOpacityDefault - setEdgeSourceArrowShapeMapping - setEdgeTargetArrowShapeMapping - setEdgeTooltipDefault - setNodeBorderOpacityDefault - setNodeBorderOpacityMapping - setNodeFillOpacityDefault - setNodeFillOpacityMapping - setNodeFontFaceDefault - setNodeFontFaceBypass - setNodeFontFaceMapping - setNodeFontSizeMapping - setNodeHeightDefault - setNodeHeightMapping - setNodeLabelDefault - setNodeLabelColorMapping - setNodeLabelOpacityDefault - setNodeLabelOpactiyMapping - setNodeTooltipDefault - setNodeTooltipBypass - setNodeWidthDefault - setNodeWidthMapping
• Bug Fixes - createSubnetwork -- #43 network suids i/o names - openSession works with current working directory -- #50
• Doc Fixes - improved visual.prop handling in mapVisualProperty -- #49,#53 user report - added file overwrite warnings to all export and save functions

RCy3 2.2.7

• Doc Fixes - vignette for phylogenetic trees

RCy3 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

RCy3 2.2.5

• Bug Fixes - createXXXFilter and applyFilter -- #40 network arg
• Doc Fixes - new filters vignette

RCy3 2.2.4

• Doc Fixes - vignettes

RCy3 2.2.3

• Doc Fixes - vignettes

RCy3 2.2.2

• Doc Fixes - new custom graphics vignette

RCy3 2.2.1

• Doc Fixes - vignettes, readme and test

RCy3 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

RCy3 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