Installation | Required Software | Example: Species specific considerations | Perform identifier mapping | Example: From proteins to genes | Example: Mixed identifiers | More advanced cases
Package: RCy3 2.33.0
Jing Chen
RCy3: Functions to Access and Control Cytoscape
Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.
Authors:
RCy3_2.33.0.tar.gz
RCy3_2.33.0.zip(r-4.7)RCy3_2.33.0.zip(r-4.6)RCy3_2.33.0.zip(r-4.5)
RCy3_2.33.0.tgz(r-4.6-any)RCy3_2.33.0.tgz(r-4.5-any)
RCy3_2.33.0.tar.gz(r-4.7-any)RCy3_2.33.0.tar.gz(r-4.6-any)
RCy3_2.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RCy3/json (API)
| # Install 'RCy3' in R: |
| install.packages('RCy3', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cytoscape/rcy3/issues
On BioConductor:RCy3-2.33.0(bioc 3.24)RCy3-2.32.0(bioc 3.23)
visualizationgraphandnetworkthirdpartyclientnetwork
Last updated from:102928c7b6. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 206 | ||
| linux-devel-x86_64 | NOTE | 159 | ||
| source / vignettes | OK | 207 | ||
| linux-release-x86_64 | NOTE | 219 | ||
| macos-release-arm64 | NOTE | 120 | ||
| macos-oldrel-arm64 | NOTE | 111 | ||
| windows-devel | NOTE | 142 | ||
| windows-release | NOTE | 100 | ||
| windows-oldrel | NOTE | 126 | ||
| wasm-release | OK | 127 |
Exports:addAnnotationBoundedTextaddAnnotationImageaddAnnotationShapeaddAnnotationTextaddCyEdgesaddCyNodesAddToGroupanalyzeNetworkapplyFilterbundleEdgescheckNotebookIsRunningcheckRunningRemoteclearEdgeBendsclearEdgePropertyBypassclearNetworkCenterBypassclearNetworkPropertyBypassclearNetworkZoomBypassclearNodeOpacityBypassclearNodePropertyBypassclearSelectioncloneNetworkcloseSessioncollapseGroupcommandEchocommandOpenDialogcommandPausecommandQuitcommandRunFilecommandsAPIcommandsGETcommandsHelpcommandSleepcommandsPOSTcommandsRuncopyVisualStylecreateColumnFiltercreateCompositeFiltercreateCytoscapejsFromNetworkcreateDegreeFiltercreateGraphFromNetworkcreateGroupcreateGroupByColumncreateIgraphFromNetworkcreateNetworkFromCytoscapejscreateNetworkFromDataFramescreateNetworkFromGraphcreateNetworkFromIgraphcreateSubnetworkcreateViewcreateVisualStylecybrowserClosecybrowserDialogcybrowserHidecybrowserListcybrowserSendcybrowserShowcybrowserVersioncyrestAPIcyrestDELETEcyrestGETcyrestPOSTcyrestPUTcytoscapeApiVersionscytoscapeFreeMemorycytoscapeMemoryStatuscytoscapeNumberOfCorescytoscapePingcytoscapeVersionInfodeleteAllNetworksdeleteAllVisualStyledeleteAnnotationdeleteDuplicateEdgesdeleteGroupdeleteNetworkdeleteSelectedEdgesdeleteSelectedNodesdeleteSelfLoopsdeleteStyleMappingdeleteTableColumndeleteVisualStylediffusionAdvanceddiffusionBasicdisableAppdockPaneldoInitializeSandboxdoRequestRemotedoSetSandboxenableAppexpandGroupexportFiltersexportImageexportJPGexportNetworkexportNetworkToNDExexportPDFexportPNGexportPSexportSVGexportVisualStylesfindRemoteCytoscapefitContentfloatPanelgetAbsSandboxPathgetAllEdgesgetAllNodesgetAllStyleMappingsgetAnnotationListgetAppInformationgetAppStatusgetAppUpdatesgetArrowShapesgetAvailableAppsgetBackgroundColorDefaultgetBrowserClientChannelgetBrowserClientJsgetCollectionListgetCollectionNamegetCollectionNetworksgetCollectionSuidgetCurrentSandboxgetCurrentSandboxNamegetCurrentSandboxPathgetCurrentStylegetDefaultSandboxgetDefaultSandboxPathgetDisabledAppsgetEdgeColorgetEdgeCountgetEdgeInfogetEdgeLineStylegetEdgeLineWidthgetEdgePropertygetEdgeSelectionColorDefaultgetEdgeTargetArrowShapegetFilterListgetFirstNeighborsgetGroupInfogetInstalledAppsgetJupyterBridgeURLgetLayoutNameMappinggetLayoutNamesgetLayoutPropertyNamesgetLayoutPropertyTypegetLayoutPropertyValuegetLineStylesgetNetworkCentergetNetworkCountgetNetworkListgetNetworkNamegetNetworkNDExIdgetNetworkPropertygetNetworkSuidgetNetworkViewsgetNetworkViewSuidgetNetworkZoomgetNodeColorgetNodeCountgetNodeHeightgetNodeLabelPositiongetNodeLabelPositionDefaultgetNodePositiongetNodePropertygetNodeSelectionColorDefaultgetNodeShapesgetNodeSizegetNodeWidthgetNotebookIsRunninggetSandboxReinitializegetSelectedEdgeCountgetSelectedEdgesgetSelectedNodeCountgetSelectedNodesgetStyleDependenciesgetStyleMappinggetTableColumnNamesgetTableColumnsgetTableColumnTypesgetTableValuegetUninstalledAppsgetVisualPropertyDefaultgetVisualPropertyNamesgetVisualStyleJSONgetVisualStyleNamesgroupAnnotationhideAllPanelshideEdgeshideNodeshidePanelhideSelectedEdgeshideSelectedNodesimportFileFromUrlimportFiltersimportNetworkFromFileimportNetworkFromNDEximportVisualStylesinstallAppinvertEdgeSelectioninvertNodeSelectionlayoutCopycatlayoutNetworklistGroupsloadTableDatalockNodeDimensionsmakeSimpleGraphmakeSimpleIgraphmapTableColumnmapVisualPropertymatchArrowColorToEdgemergeNetworksnotebookExportShowImagenotebookShowImageopenAppStoreopenSessionpaletteColorBrewerAccentpaletteColorBrewerBluespaletteColorBrewerBrBGpaletteColorBrewerBuGnpaletteColorBrewerBuPupaletteColorBrewerDark2paletteColorBrewerGnBupaletteColorBrewerGreenspaletteColorBrewerGreyspaletteColorBrewerOrangespaletteColorBrewerOrRdpaletteColorBrewerPairedpaletteColorBrewerPastel1paletteColorBrewerPastel2paletteColorBrewerPiYGpaletteColorBrewerPRGnpaletteColorBrewerPuBupaletteColorBrewerPuBuGnpaletteColorBrewerPuOrpaletteColorBrewerPuRdpaletteColorBrewerPurplespaletteColorBrewerRdBupaletteColorBrewerRdPupaletteColorBrewerRdYlBupaletteColorBrewerRedspaletteColorBrewerSet1paletteColorBrewerSet2paletteColorBrewerSet3paletteColorBrewerYlGnpaletteColorBrewerYlGnBupaletteColorBrewerYlOrBrpaletteColorBrewerYlOrRdpaletteColorRandompaletteColorVirdisRemoveFromGroupremoveNodeCustomGraphicsrenameNetworkrenameTableColumnresetDefaultSandboxrotateLayoutrunningRemoteChecksandboxGetFileInfosandboxGetFromsandboxInitializersandboxRemovesandboxRemoveFilesandboxSendTosandboxSetsandboxUrlTosaveSessionscaleLayoutselectAllselectAllEdgesselectAllNodesselectEdgesselectEdgesAdjacentToNodesselectEdgesAdjacentToSelectedNodesselectEdgesConnectingSelectedNodesselectFirstNeighborsselectNodesselectNodesConnectedBySelectedEdgessetBackgroundColorDefaultsetCatchupFilterSecssetCatchupNetworkSecssetCollectionNamesetCurrentNetworksetCurrentSandboxsetCurrentViewsetDefaultSandboxsetDefaultSandboxPathsetEdgeColorBypasssetEdgeColorDefaultsetEdgeColorMappingsetEdgeFontFaceBypasssetEdgeFontFaceDefaultsetEdgeFontFaceMappingsetEdgeFontSizeBypasssetEdgeFontSizeDefaultsetEdgeFontSizeMappingsetEdgeLabelBypasssetEdgeLabelColorBypasssetEdgeLabelColorDefaultsetEdgeLabelColorMappingsetEdgeLabelDefaultsetEdgeLabelMappingsetEdgeLabelOpacityBypasssetEdgeLabelOpacityDefaultsetEdgeLabelOpacityMappingsetEdgeLineStyleBypasssetEdgeLineStyleDefaultsetEdgeLineStyleMappingsetEdgeLineWidthBypasssetEdgeLineWidthDefaultsetEdgeLineWidthMappingsetEdgeOpacityBypasssetEdgeOpacityDefaultsetEdgeOpacityMappingsetEdgePropertyBypasssetEdgeSelectionColorDefaultsetEdgeSourceArrowColorBypasssetEdgeSourceArrowColorDefaultsetEdgeSourceArrowColorMappingsetEdgeSourceArrowMappingsetEdgeSourceArrowShapeBypasssetEdgeSourceArrowShapeDefaultsetEdgeSourceArrowShapeMappingsetEdgeTargetArrowColorBypasssetEdgeTargetArrowColorDefaultsetEdgeTargetArrowColorMappingsetEdgeTargetArrowMappingsetEdgeTargetArrowShapeBypasssetEdgeTargetArrowShapeDefaultsetEdgeTargetArrowShapeMappingsetEdgeTooltipBypasssetEdgeTooltipDefaultsetEdgeTooltipMappingsetLayoutPropertiessetModelPropagationSecssetNetworkCenterBypasssetNetworkPropertyBypasssetNetworkZoomBypasssetNodeBorderColorBypasssetNodeBorderColorDefaultsetNodeBorderColorMappingsetNodeBorderOpacityBypasssetNodeBorderOpacityDefaultsetNodeBorderOpacityMappingsetNodeBorderWidthBypasssetNodeBorderWidthDefaultsetNodeBorderWidthMappingsetNodeColorBypasssetNodeColorDefaultsetNodeColorMappingsetNodeComboOpacityMappingsetNodeCustomBarChartsetNodeCustomBoxChartsetNodeCustomHeatMapChartsetNodeCustomLinearGradientsetNodeCustomLineChartsetNodeCustomPieChartsetNodeCustomPositionsetNodeCustomRadialGradientsetNodeCustomRingChartsetNodeFillOpacityBypasssetNodeFillOpacityDefaultsetNodeFillOpacityMappingsetNodeFontFaceBypasssetNodeFontFaceDefaultsetNodeFontFaceMappingsetNodeFontSizeBypasssetNodeFontSizeDefaultsetNodeFontSizeMappingsetNodeHeightBypasssetNodeHeightDefaultsetNodeHeightMappingsetNodeLabelBypasssetNodeLabelColorBypasssetNodeLabelColorDefaultsetNodeLabelColorMappingsetNodeLabelDefaultsetNodeLabelMappingsetNodeLabelOpacityBypasssetNodeLabelOpacityDefaultsetNodeLabelOpacityMappingsetNodeLabelPositionBypasssetNodeLabelPositionDefaultsetNodeOpacityBypasssetNodePositionBypasssetNodePropertyBypasssetNodeSelectionColorDefaultsetNodeShapeBypasssetNodeShapeDefaultsetNodeShapeMappingsetNodeSizeBypasssetNodeSizeDefaultsetNodeSizeMappingsetNodeTooltipBypasssetNodeTooltipDefaultsetNodeTooltipMappingsetNodeWidthBypasssetNodeWidthDefaultsetNodeWidthMappingsetNotebookIsRunningsetSandboxReinitializesetStyleDependenciessetVisualPropertyDefaultsetVisualStylespoofResponsesyncNodeCustomGraphicsSizetoggleGraphicsDetailsungroupAnnotationunhideAllunhideEdgesunhideNodesuninstallAppUpdateAnnotationBoundedTextupdateAnnotationImageupdateAnnotationShapeupdateAnnotationTextupdateAppupdateGroupAnnotationupdateNetworkInNDExupdateStyleDefaultsupdateStyleMapping
Dependencies:askpassbackportsbase64encbase64urlBiocGenericsbitopscaToolsclicrayoncurldigestevaluatefastmapfsgenericsgluegplotsgraphgtoolshtmltoolshttrIRdisplayIRkerneljsonliteKernSmoothlifecyclemimeopensslpbdZMQpillarR6RColorBrewerRCurlreprRJSONIOrlangstringisysutf8uuidvctrsXML
Identifier mapping
Last update: 2024-04-05
Started: 2018-04-07
Jupyter Bridge and RCy3
How Jupyter Bridge works | Sandbox | Prerequisites (Local machine) | Prerequisites (Cloud server) | Installation | Connect to local Cytoscape | Check connection | Use case: Run differentially expressed genes network analysis in the cloud
Last update: 2022-04-07
Started: 2022-04-07
Cancer networks and data
Installation | Required Software | Getting Disease Networks | Query STRING database by disease to generate networks | Breast cancer | Ovarian cancer | Interacting with Cytoscape | Get list of networks | Layout network | List of layout algorithms available | Layout with parameters! | Get table data from network | Retrieve disease scores | Plot distribution and pick threshold | Generate subnetworks | Visualizing data on networks | Load datasets | Breast Cancer Datset | Visual styles | Visualize expression data | Visualize mutation data | Subnetwork based on diffusion from heavily mutated nodes | Ovarian Cancer Datset | Saving, sharing and publishing | Saving a Cytoscape session file | Saving high resolution image files
Last update: 2021-09-27
Started: 2018-03-16
Filtering Networks
Installation | Prerequisites | Get network from STRING | Filtering by degree | Creating a degree filter | Creating a subnetwork from a selection | Filtering by attribute | Creating a column filter | Combining filters | Hiding filtered nodes
Last update: 2019-12-05
Started: 2018-11-28
Overview of RCy3
Installation | Prerequisites | Getting started | My first network | Switch styles | My own style | Bioconductor graph example | Add node attributes | Modifying the display: defaults and mappings | Selecting nodes | Saving and export | Saving high resolution image files | Browse available functions, commands and arguments | More examples | Development | Credits | References
Last update: 2019-09-28
Started: 2018-03-18
Phylogenetic-trees
Installation | Prerequisites | Trees to Networks | Network to Cytoscape | Edge Length as Distance
Last update: 2019-03-08
Started: 2019-03-08
Custom Graphics and Labels
Installation | Prerequisites | Open Sample | Set style and node color | Custom Graphics | Bar chart | Stripes | Pie chart | Enhanced Graphics | Install enhancedGraphics | Define new label | Map and position label
Last update: 2018-11-18
Started: 2018-11-17
Cytoscape and igraph
Installation | Required Software | From igraph to Cytoscape | From Cytoscape to igraph
Last update: 2018-07-14
Started: 2018-03-18
Upgrading existing scripts
Installation | Prerequisites | Big changes for RCy3 | Where to start | Upgrading Existing Scripts | NEWS | Example upgrades | Example: displayGraph | Example: cyPlot | Example: loading nodeData | Example: setDefaults | Example: Rule based mapping | Example: Selecting nodes | Example: Saving and exporting | Going forward
Last update: 2018-07-14
Started: 2018-04-08
Group nodes
Installation | Required Software | Background | Example
Last update: 2018-07-14
Started: 2018-06-24
Cytoscape and NDEx
Installation | Prerequisites | Finding networks | Viewing networks | Sending networks to NDEx
Last update: 2018-06-29
Started: 2018-04-22
Network functions and visualization
Installation | Required Software | Read a data set. | Common iGraph functions | Add attributes to network | Let check it out in Cytoscape | Let's decide on a layout | Next, we can visualize our data | Track versions for your records
Last update: 2018-06-25
Started: 2018-03-16
Cytoscape and graphNEL
Installation | Required Software | From graphNEL to Cytoscape | From Cytoscape to GraphNEL
Last update: 2018-06-24
Started: 2018-02-18
Importing data
Installation | Required Software | Always Start with a Network | Import Data
Last update: 2018-06-24
Started: 2018-01-14
