Changes in version 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 Changes in version 2.12.x + 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 Changes in version 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 Changes in version 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 Changes in version 2.8.0 + New functions: - mergeNetworks - analyzeNetwork + Better messaging for... - App-related functions, like installApp - When style changes are applied to "default" style Changes in version 2.6.x + 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 Changes in version 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 Changes in version 2.4.4 + Bug Fixes - filter functions -- #73 wrong params Changes in version 2.4.3 + Bug Fixes - import functions -- #62 fixed default directory Changes in version 2.4.2 + Bug Fixes - getEdgeInfo -- #61 missing function Changes in version 2.4.1 + Bug Fixes - getLayoutPropertyNames -- #59 fixed returned values - createNetworkFromIgraph -- #58 flatten list attributes to strings Changes in version 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 Changes in version 2.2.7 + Doc Fixes - vignette for phylogenetic trees Changes in version 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 version 2.2.5 + Bug Fixes - createXXXFilter and applyFilter -- #40 network arg + Doc Fixes - new filters vignette Changes in version 2.2.4 + Doc Fixes - vignettes Changes in version 2.2.3 + Doc Fixes - vignettes Changes in version 2.2.2 + Doc Fixes - new custom graphics vignette Changes in version 2.2.1 + Doc Fixes - vignettes, readme and test Changes in version 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