Files in RCy3
Functions to Access and Control Cytoscape

NEWS
LICENSE
DESCRIPTION
README.md
NAMESPACE
.travis.yml
inst/CITATION
inst/unitTests/test_RCy3.R
inst/doc/Network-functions-and-visualization.html
inst/doc/Filtering-Networks.Rmd inst/doc/Cytoscape-and-iGraph.R inst/doc/Overview-of-RCy3.R
inst/doc/Importing-data.html
inst/doc/Cytoscape-and-NDEx.Rmd
inst/doc/Custom-Graphics.html
inst/doc/Cytoscape-and-iGraph.Rmd
inst/doc/Cytoscape-and-NDEx.html
inst/doc/Identifier-mapping.Rmd inst/doc/Importing-data.R inst/doc/Group-nodes.R
inst/doc/Upgrading-existing-scripts.html
inst/doc/Identifier-mapping.R
inst/doc/Cancer-networks-and-data.html
inst/doc/Custom-Graphics.Rmd inst/doc/Overview-of-RCy3.Rmd inst/doc/Network-functions-and-visualization.Rmd
inst/doc/Cytoscape-and-iGraph.html
inst/doc/Cytoscape-and-graphNEL.html
inst/doc/Cytoscape-and-graphNEL.Rmd
inst/doc/Identifier-mapping.html
inst/doc/Overview-of-RCy3.html
inst/doc/Upgrading-existing-scripts.R inst/doc/Cancer-networks-and-data.Rmd inst/doc/Cytoscape-and-graphNEL.R inst/doc/Filtering-Networks.R inst/doc/Cytoscape-and-NDEx.R
inst/doc/Filtering-Networks.html
inst/doc/Custom-Graphics.R inst/doc/Importing-data.Rmd inst/doc/Cancer-networks-and-data.R inst/doc/Upgrading-existing-scripts.Rmd inst/doc/Group-nodes.Rmd inst/doc/Network-functions-and-visualization.R
inst/doc/Group-nodes.html
inst/extdata/tutorial-ovc-mut-dataset.robj
inst/extdata/tutorial-brc-expr-mean-dataset.robj
inst/extdata/galFiltered.sif
inst/extdata/tutorial-brc-mut-dataset.robj
inst/extdata/lesmis.txt
inst/extdata/virus_prok_cor_abundant.tsv
inst/extdata/phage_ids_with_affiliation.tsv
inst/extdata/galExpData.csv
inst/extdata/prok_tax_from_silva.tsv
inst/extdata/tutorial-ovc-expr-mean-dataset.robj
vignettes/Filtering-Networks.Rmd vignettes/Cytoscape-and-NDEx.Rmd vignettes/Cytoscape-and-iGraph.Rmd vignettes/Identifier-mapping.Rmd vignettes/Custom-Graphics.Rmd vignettes/Overview-of-RCy3.Rmd vignettes/Network-functions-and-visualization.Rmd vignettes/Cytoscape-and-graphNEL.Rmd vignettes/Cancer-networks-and-data.Rmd vignettes/Importing-data.Rmd vignettes/Upgrading-existing-scripts.Rmd vignettes/Group-nodes.Rmd R/Collections.R R/Tools.R R/Tables.R R/Styles.R R/StyleMappings.R R/StyleDependencies.R R/StyleDefaults.R R/RCy3.R R/RCy3-utils.R R/CyNDEx.R R/Session.R R/Layouts.R R/StyleValues.R R/Apps.R R/Networks.R R/Groups.R R/NetworkSelection.R R/RCy3-deprecated.R R/Commands.R R/UserInterface.R R/StyleBypasses.R R/Filters.R R/CytoscapeSystem.R R/NetworkViews.R man/getEdgeSelectionColorDefault.Rd man/getAppInformation.Rd man/updateStyleDefaults.Rd man/saveNetwork-defunct.Rd man/setNodeSelectionColorDefault.Rd man/diffusionBasic.Rd man/selectEdgesAdjacentToSelectedNodes.Rd man/clearNetworkPropertyBypass.Rd man/getLayoutNameMapping.Rd man/deleteWindow-defunct.Rd man/commandsRun.Rd man/mapTableColumn.Rd man/getVisualPropertyDefault.Rd man/deleteStyleMapping.Rd man/clearNodePropertyBypass.Rd man/layoutCopycat.Rd man/deleteDuplicateEdges.Rd man/importVisualStyles.Rd man/setZoom-defunct.Rd man/cybrowserSend.Rd man/setBackgroundColorDefault.Rd man/getDisabledApps.Rd man/deleteNetwork.Rd man/selectAllNodes.Rd man/setNodeColorBypass.Rd man/createNetworkFromGraph.Rd man/dockPanel.Rd man/setNodeLabelOpacityBypass.Rd man/setLayoutProperties.Rd man/saveImage-defunct.Rd man/cloneNetwork.Rd man/RCy3.Rd man/selectEdgesConnectedBySelectedNodes-defunct.Rd man/cyrestPUT.Rd man/getSelectedEdgeCount.Rd man/setVisualStyle.Rd man/setEdgeLabelBypass.Rd man/getCenter-defunct.Rd man/getGroupInfo.Rd man/setEdgeSourceArrowShapeBypass.Rd man/deleteTableColumn.Rd man/setNodeBorderOpacityBypass.Rd man/copyVisualStyle.Rd man/createVisualStyle.Rd man/setEdgeLineStyleMapping.Rd man/getTableColumns.Rd man/setEdgeTargetArrowShapeBypass.Rd man/setEdgeLabelColorBypass.Rd man/getAvailableApps.Rd man/cybrowserShow.Rd man/setNodeShapeMapping.Rd man/getEdgeProperty.Rd man/getWindowID-defunct.Rd man/createNetworkFromIgraph.Rd man/getEdgeColor.Rd man/getCommandNames-defunct.Rd man/hideSelectedEdges.Rd man/commandQuit.Rd man/invertNodeSelection.Rd man/getNetworkZoom.Rd man/hideAllPanels.Rd man/getNodeCount.Rd man/setEdgeFontSizeDefault.Rd man/setEdgeTargetArrowShapeDefault.Rd man/bundleEdges.Rd man/getNetworkNDExId.Rd man/exportNetworkToNDEx.Rd man/setEdgeColorBypass.Rd man/commandEcho.Rd man/createIgraphFromNetwork.Rd man/matchArrowColorToEdge.Rd man/getFirstNeighbors.Rd man/getUninstalledApps.Rd man/collapseGroup.Rd man/setNodeCustomHeatMapChart.Rd man/hidePanel.Rd man/setNetworkPropertyBypass.Rd man/getCollectionSuid.Rd man/setNodeCustomLineChart.Rd man/exportFilters.Rd man/mapVisualProperty.Rd man/createColumnFilter.Rd man/setEdgeLabelOpacityBypass.Rd man/setEdgeLineWidthMapping.Rd man/removeNodeCustomGraphics.Rd man/setEdgeSelectionColorDefault.Rd man/deleteGroup.Rd man/setEdgeSourceArrowColorMapping.Rd man/getEdgeAttribute-defunct.Rd man/setVisualPropertyDefault.Rd man/lockNodeDimensions.Rd man/setNodeFontSizeBypass.Rd man/setEdgeLineStyleBypass.Rd man/floatPanel.Rd man/setNodeSizeMapping.Rd man/getLineStyles.Rd man/commandsHelp.Rd man/cybrowserClose.Rd man/deleteVisualStyle.Rd man/getTableColumnTypes.Rd man/getNetworkViews.Rd man/cyrestAPI.Rd man/getAllEdges.Rd man/getSelectedNodeCount.Rd man/cytoscapePing.Rd man/getWindowList-defunct.Rd man/cybrowserVersion.Rd man/setStyleDependencies.Rd man/getLayoutNames.Rd man/importFilters.Rd man/deleteAllWindows-defunct.Rd man/ping-defunct.Rd man/deleteSelfLoops.Rd man/setEdgeSourceArrowMapping.Rd man/createWindowFromSelection-defunct.Rd man/cytoscapeVersionInfo.Rd man/renameCytoscapeNetwork-defunct.Rd man/createDegreeFilter.Rd man/createWindow-defunct.Rd man/createGraphFromNetwork.Rd man/setNodeShapeDefault.Rd man/existing.CytoscapeWindow-defunct.Rd man/invertEdgeSelection.Rd man/setNodeHeightBypass.Rd man/setNodeSizeBypass.Rd man/getNodeProperty.Rd man/getNetworkProperty.Rd man/setNodeCustomPieChart.Rd man/clearNetworkZoomBypass.Rd man/commandsPOST.Rd man/getCommandNamesWithinNamespace-defunct.Rd man/CytoscapeConnection-defunct.Rd man/setNodeWidthBypass.Rd man/getNodeHeight.Rd man/setNodeFontSizeDefault.Rd man/getTableValue.Rd man/setEdgeOpacityMapping.Rd man/getVisualStyleNames.Rd man/setNodeLabelMapping.Rd man/setEdgeColorDefault.Rd man/exportImage.Rd man/cybrowserDialog.Rd man/renameNetwork.Rd man/AddToGroup.Rd man/getEdgeLineWidth.Rd man/makeSimpleIgraph.Rd man/RemoveFromGroup.Rd man/selectNodes.Rd man/getStyleDependencies.Rd man/setNodeTooltipMapping.Rd man/setCenter-defunct.Rd man/unhideEdges.Rd man/cytoscapeMemoryStatus.Rd man/commandsAPI.Rd man/setEdgeLineWidthBypass.Rd man/setEdgeColorMapping.Rd man/getNodeColor.Rd man/hideSelectedNodes.Rd man/getNodeSelectionColorDefault.Rd man/selectFirstNeighborsOfSelectedNodes-defunct.Rd man/updateApp.Rd man/selectEdges.Rd man/layoutNetwork.Rd man/commandOpenDialog.Rd man/getSelectedNodes.Rd man/CytoscapeWindow-defunct.Rd man/setEdgeTargetArrowColorMapping.Rd man/addCyEdges.Rd man/setNodeComboOpacityMapping.Rd man/createNetworkFromDataFrames.Rd man/setEdgeSourceArrowColorBypass.Rd man/setEdgeFontSizeBypass.Rd man/createSubnetwork.Rd man/setEdgeTargetArrowColorBypass.Rd man/commandsGET.Rd man/syncNodeCustomGraphicsSize.Rd man/makeSimpleGraph.Rd man/setEdgeSourceArrowColorDefault.Rd man/setNodePropertyBypass.Rd man/setNodeBorderColorDefault.Rd man/getArrowShapes.Rd man/diffusionAdvanced.Rd man/deleteAllNetworks.Rd man/setNodeSizeDefault.Rd man/getEdgeTargetArrowShape.Rd man/getEdgeCount.Rd man/getNetworkName.Rd man/cybrowserHide.Rd man/getAppUpdates.Rd man/getDirectlyModifiableVisualProperties-defunct.Rd man/getVisualPropertyNames.Rd man/setCurrentView.Rd man/createCompositeFilter.Rd man/commandSleep.Rd man/renameTableColumn.Rd man/getNetworkCenter.Rd man/updateStyleMapping.Rd man/unhideAll.Rd man/getInstalledApps.Rd man/unhideNodes.Rd man/redraw-defunct.Rd man/cytoscapeFreeMemory.Rd man/getLayoutPropertyNames.Rd man/pluginVersion-defunct.Rd man/setNodeColorMapping.Rd man/setEdgeTooltipBypass.Rd man/importNetworkFromNDEx.Rd man/setNodeCustomLinearGradient.Rd man/setEdgeLineStyleDefault.Rd man/getSelectedEdges.Rd man/getNodeAttribute-defunct.Rd man/setNodeCustomPosition.Rd man/setNodeCustomBoxChart.Rd man/setNetworkZoomBypass.Rd man/toggleGraphicsDetails.Rd man/cybrowserList.Rd man/setEdgeLabelMapping.Rd man/setNodeFillOpacityBypass.Rd man/getNodeAttributeNames-defunct.Rd man/selectNodesConnectedBySelectedEdges.Rd man/disableApp.Rd man/setNodeColorDefault.Rd man/getNetworkCount.Rd man/setNodeOpacityBypass.Rd man/clearNodeOpacityBypass.Rd man/applyFilter.Rd man/setCurrentNetwork.Rd man/getNodeShapes.Rd man/deleteSelectedNodes.Rd man/getZoom-defunct.Rd man/setNodeLabelColorDefault.Rd man/clearEdgePropertyBypass.Rd man/getGraphFromCyWindow-defunct.Rd man/fitContent.Rd man/exportVisualStyles.Rd man/setNodeBorderWidthDefault.Rd man/setNodeCustomRadialGradient.Rd man/setNodeBorderColorMapping.Rd man/cytoscapeNumberOfCores.Rd man/getBackgroundColorDefault.Rd man/installApp.Rd man/getTableColumnNames.Rd man/getCollectionList.Rd man/getNetworkList.Rd man/setNodeShapeBypass.Rd man/cyrestGET.Rd man/showGraphicsDetails-defunct.Rd man/createGroup.Rd man/importNetworkFromFile.Rd man/setNodeBorderWidthBypass.Rd man/expandGroup.Rd man/setEdgeLineWidthDefault.Rd man/deleteSelectedEdges.Rd man/setEdgePropertyBypass.Rd man/cyrestPOST.Rd man/getNodeSize.Rd man/getCollectionNetworks.Rd man/setNodeLabelBypass.Rd man/cytoscapeApiVersions.Rd man/sfn-defunct.Rd man/setNodeCustomBarChart.Rd man/setEdgeTargetArrowMapping.Rd man/getAppStatus.Rd man/updateNetworkInNDEx.Rd man/getLayoutPropertyType.Rd man/setEdgeOpacityBypass.Rd man/hideEdges.Rd man/uninstallApp.Rd man/commandPause.Rd man/setEdgeSourceArrowShapeDefault.Rd man/openSession.Rd man/setNodeLabelColorBypass.Rd man/listGroups.Rd man/setNetworkCenterBypass.Rd man/getNetworkViewSuid.Rd man/getEdgeAttributeNames-defunct.Rd man/getAllNodes.Rd man/selectAllEdges.Rd man/saveSession.Rd man/setEdgeTooltipMapping.Rd man/getNetworkSuid.Rd man/fitSelectedContent-defunct.Rd man/setEdgeFontFaceBypass.Rd man/commandRunFile.Rd man/setNodeBorderWidthMapping.Rd man/openAppStore.Rd man/closeSession.Rd man/exportNetwork.Rd man/deleteEdgeAttribute-defunct.Rd man/getAllNodeAttributes-defunct.Rd man/setEdgeTargetArrowColorDefault.Rd man/clearSelection.Rd man/getLayoutPropertyValue.Rd man/clearNetworkCenterBypass.Rd man/setNodeCustomRingChart.Rd man/addCyNodes.Rd man/getAllEdgeAttributes-defunct.Rd man/getCollectionName.Rd man/getWindowCount-defunct.Rd man/getFilterList.Rd man/getNodeWidth.Rd man/getEdgeLineStyle.Rd man/selectEdgesConnectingSelectedNodes.Rd man/enableApp.Rd man/cyrestDELETE.Rd man/setNodeBorderColorBypass.Rd man/selectFirstNeighbors.Rd man/deleteNodeAttribute-defunct.Rd man/hideNodes.Rd man/loadTableData.Rd man/copyCytoscapeNetwork-defunct.Rd
build/vignette.rds
tests/runTests.R
RCy3 documentation built on Dec. 8, 2018, 6 p.m.