Changes in version 2.30.0 o fix clearNodePropertyBypass, #229 Changes in version 2.28.0 o No changes since version 2.26.0. Changes in version 2.26.0 o Added documentation & checks for super-long commands - suggest users to use commandsPost() when URI too long o Bug fixes: - check for Inf and -Inf in double columns during loadTableData, #224 - fix missing base.url in some functions o Add test functions Changes in version 2.24.0 o Use stringi to replace uchardet o Add test functions o Doc fixes: - add "c" to anchor choices o Bug fixes: - fix setNodePositionBypass to support network and base.url - use viridis color palette for continuous mapping, #210 Changes in version 2.22.0 o New functions: - setNodePositionBypass - getNodeLabelPosition - setNodeLabelPositionBypass - setNodeLabelPositionDefault - getNodeLabelPositionDefault - rotateLayout - scaleLayout o Update .verifySupportedVersions to support x.y.z o 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 Changes in version 2.20.0 o Add a delay in mergeNetworks method - Wait for Cytoscape to finish adding annotations column to Network table o Bug fixes: - ellipsis args in createNetworkFromDataFrames, #195 - setNodeColorBypass: List of hex colors, #188 Changes in version 2.18.0 o New functions: - exportPNG - exportJPG - exportPDF - exportPS - exportSVG - importFileFromUrl - selectEdgesAdjacentToNodes Changes in version 2.16.0 o Faster selectAll* functions o Add a new vignette about cloud notebooks with RCy3 o Doc fixes: - Conflicting Brightness/Contrast documentation, #172 - Conflicting Opacity documentation, #173 - updateAnnotationText cleanup, #177 o New functions: - createView - selectAll o 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 Changes in version 2.14.0 o Cleaned up dependencies, dramatically reducing RCy3 package installation time o New functions: - add and update Annotations - uniqueList parameter added to edgeNameToEdgeSUID and nodeNameToNodeSUID, #139 o Bug fixes: - loadTableData now works with tibbles, #143 - sandboxSendTo now works with cys and png, #138 - .verifySupportedVersions fixed comparisons, #152 Changes in version 2.12 o Doc fixes - note about metabolite databases, #146 o Bug fixes - createVisualStyle for notebooks, #145 - regression bug for relative paths, #141 - filepath handling in export functions, #122 - Sys.sleep added to setVisualStyle, #137 Changes in version 2.12.0 o 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 o 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 o New parameters: - overwrite_file added to export functions - apply added to create_*_filter functions - ndex.url and ndex.version added to CyNDEx functions o Consistent interchangeable handling of node|edge|network names and SUIDs o createNetworkFromDataframes plays nice with tibbles o Bug fixes: - .edgeNameToEdgeSUID revamped to better handle duplicate edge names Changes in version 2.10.0 o New functions: - getCurrentStyle, #15 o Added Sys.sleep to buggy CyREST steps in... - createNetworkFromDataFrames, #98 - importNetworkFromFile - importNetworkFromNDEx - exportNetworkToNDEx - updateNetworkInNDEx - importFilters - create***Filter - applyFilter - updateStyleMapping - setVisualPropertyDefault o Refactored getNetworkViewSuid o Handled special 404 cases in .cyError o Bug fix #94: added base.url param o Overhauled error handling and messaging Changes in version 2.8.0 o New functions: - mergeNetworks - analyzeNetwork o Better messaging for... - App-related functions, like installApp - When style changes are applied to "default" style Changes in version 2.6 o Doc Fixes - Roxygen update and man pages - Fixes to unitTests o Bug Fixes - getSelectedNodes/Edges -- #82 fixed missing param in usage - added missing base.url args -- #88 Changes in version 2.6.0 o New functions: - createGroupByColumn - clearEdgeBends - getNodePosition o New parameter to return SUIDs for - getSelectedNodes - getSelectedEdges o Node and edge property values returned as named lists o Faster results for getting all node and edge property values, #78 o More robust handling of file type in export functions o More robust handling of dataframes in createNetworkFromDataFrames o New support for loading list data o Doc Fixes - added Filters to Overview vignette - improved file type handling descriptions Changes in version 2.4.4 o Bug Fixes - filter functions -- #73 wrong params Changes in version 2.4.3 o Bug Fixes - import functions -- #62 fixed default directory Changes in version 2.4.2 o Bug Fixes - getEdgeInfo -- #61 missing function Changes in version 2.4.1 o Bug Fixes - getLayoutPropertyNames -- #59 fixed returned values - createNetworkFromIgraph -- #58 flatten list attributes to strings Changes in version 2.4.0 o 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 o Bug Fixes - createSubnetwork -- #43 network suids i/o names - openSession works with current working directory -- #50 o Doc Fixes - improved visual.prop handling in mapVisualProperty -- #49,#53 user report - added file overwrite warnings to all export and save functions Changes in version 2.2.7 o Doc Fixes - vignette for phylogenetic trees Changes in version 2.2.6 o Bug Fixes - saveSession, exportXXX -- #39 default to working directory - createNetworkFromDataFrame and .edgeNameToSuids -- #41 multigraph support - BiocCheck errors and warnings -- #42 o Doc Fixes - added tests for multigraphs Changes in version 2.2.5 o Bug Fixes - createXXXFilter and applyFilter -- #40 network arg o Doc Fixes - new filters vignette Changes in version 2.2.4 o Doc Fixes - vignettes Changes in version 2.2.3 o Doc Fixes - vignettes Changes in version 2.2.2 o Doc Fixes - new custom graphics vignette Changes in version 2.2.1 o Doc Fixes - vignettes, readme and test Changes in version 2.2.0 o New functions to remove duplicate edges - deleteDuplicateEdges - deleteSelfLoops o New node selection function - selectNodesConnectedBySelectedEdges o New visual style management functions - importVisualStyles - deleteVisualStyle - deleteStyleMapping o New edge bundling function - bundleEdges o New custom graphics options for nodes - setNodeCustomBarChart - setNodeCustomBoxChart - setNodeCustomHeatMapChart - setNodeCustomLineChart - setNodeCustomPieChart - setNodeCustomRingChart - setNodeCustomLinearGradient - setNodeCustomRadialGradient - setNodeCustomPosition - removeNodeCustomGraphics o New filter functions - applyFilter - createColumnFilter - createCompositeFilter - createDegreeFilter - getFilterList - exportFilters - importFilters o Improved speed on bulk node and edge property bypasses o Bug Fixes - selectEdgesConnectingSelectedNodes -- set default by.col = 'name' - setEdgeLineWidthMapping -- fixes input type - getGroupInfo -- works without collapsing first - getTableColumns -- work with List type columns o 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(). o Deprecated - Nothing o Defunct - Previously deprecated functions in v2.0 from older 1.x version of the package Changes in version 2.0.0 o New converter functions between Cytoscape and iGraph - createIgraphFromNetwork - createNetworkFromIgraph o New converter functions between Cytoscape and R data.frames - createNetworkFromDataFrames o New converter functions between Cytoscape and Bioconductor GraphNEL - createNetworkFromGraph - createGraphFromNetwork - addGraphToNetwork o Fixed visual style "Direct" functions to set persistent bypass values - setNodePropertyBypass - setEdgePropertyBypass - see all setNode***Bypass and setEdge***Bypass functions o Streamlined interfaces to CyREST and Commands API - cyrestGET - cyrestPUT - cyrestPOST - cyrestDELETE - cyrestAPI - commandsGET - commandsPOST - commandsAPI - commandsHelp o Optional network parameter supports calls to "current" or specified Cytoscape network by name or SUID o New functions for importing/exporting tabular data into/out of Cytoscape - getTableColumns - loadTableData o New function for batch setting visual style property mappings - mapVisualProperty o Access to Cytoscape System information - cytoscapeVersionInfo - cytoscapeApiVersions - cytoscapeNumberOfCores - cytoscapeMemoryStatus - cytoscapeFreeMemory o Updated layoutCopyCat feature o Update network management functions - createSubnetwork - cloneNetwork - renameNetwork - importNetworkFromFile o Updated selection features - selectFirstNeighbors - selectEdgesConnectingSelectedNodes - selectEdgesAdjacentToSelectedNodes o New Cytoscape session functions - openSession - closeSession o Overhauled visual style settings to match Cytoscape's Defaults, Mappings, and Bypasses o Added style dependency functions, in addition to lockNodeDimensions - matchArrowColorToEdge - syncNodeCustomGraphicsSize o New set of functions for retrieving current visual property Values for nodes, edges and networks. o New functions for network-level Visual Property Defaults, Bypasses and Values. o Streamlined data table loading and retrieval o New functions for installing and managing Cytoscape Apps, e.g., - installApp - uninstallApp - udpateApp - getInstalledApps - getAvailableApps - getAppUpdates - getAppStatus o New functions for network Collections - getCollectionList - getCollectionName - getCollectionSuid - getCollectionNetworks o New functions for accessing NDEx via CyNDEx2 - importNetworkFromNDEx - exportNetworkToNDEx - updateNetworkInNDEx - getNetworkNDExId o For Developers - Reorganized functions into files corresponding to CyREST API, e.g., Collections, CytoscapeSystem, Layouts, Networks, etc. o Normalized all documentation using roxygen2 o Streamlined interfaces to CyREST and Commands API (see above), greatly facilitating the implementation of any new functions matching CyREST or Command API additions o Reverted all single-instance methods to simple functions, replacing class-based signatures with simple default values o Established handy functions for validating network and view SUIDs - getNetworkName - getNetworkSuid - getNetworkViewSuid o Deprecated - Outdated function names o Defunct - CytoscapeConnection and CytoscapeWindow classes, functions and parameters