Man pages for tmuetze/Bioconductor_RCy3_the_new_RCytoscape
Display and manipulate graphs in Cytoscape >= 3.3.0
| addCyEdge | addCyEdge |
| addCyNode | addCyNode |
| addGraphToGraph | addGraphToGraph |
| clearSelection | clearSelection |
| connectToNewestCyWindow | Creates a connection to the newest Cytoscape window so that... |
| copyCytoscapeNetwork | Copy a Cytoscape Network |
| copyVisualStyle | copyVisualStyle |
| createWindow | createWindow |
| createWindowFromSelection | createWindowFromSelection |
| cy2.edge.names | cy2.edge.names |
| cyPlot | cyPlot |
| CytoscapeConnection | CytoscapeConnection |
| CytoscapeConnectionClass-class | Class "CytoscapeConnectionClass" |
| CytoscapeWindow | CytoscapeWindow |
| CytoscapeWindowClass-class | Class "CytoscapeWindowClass" |
| deleteAllWindows | deleteAllWindows |
| deleteEdgeAttribute | deleteEdgeAttribute |
| deleteNodeAttribute | deleteNodeAttribute |
| deleteSelectedEdges | deleteSelectedEdges |
| deleteSelectedNodes | deleteSelectedNodes |
| deleteWindow | deleteWindow |
| demoSimpleGraph | demoSimpleGraph |
| displayGraph | displayGraph |
| dockPanel | dockPanel |
| eda | eda |
| eda.names | eda.names |
| existing.CytoscapeWindow | existing.CytoscapeWindow |
| fitContent | fitContent |
| fitSelectedContent | fitSelectedContent |
| floatPanel | floatPanel |
| getAdjacentEdgeNames | getAdjacentEdgeNames |
| getAllEdgeAttributes | getAllEdgeAttributes |
| getAllEdges | getAllEdges |
| getAllNodeAttributes | getAllNodeAttributes |
| getAllNodes | getAllNodes |
| getArrowShapes | getArrowShapes |
| getAttributeClassNames | getAttributeClassNames |
| getCenter | getCenter |
| getCommandNames | Gets commands available from within cytoscape from functions... |
| getCommandsWithinNamespace | Gets commands available from within a namespace in Cytoscape... |
| getDefaultBackgroundColor | getDefaultBackgroundColor |
| getDefaultEdgeReverseSelectionColor | getDefaultEdgeReverseSelectionColor |
| getDefaultEdgeSelectionColor | getDefaultEdgeSelectionColor |
| getDefaultNodeReverseSelectionColor | getDefaultNodeReverseSelectionColor |
| getDefaultNodeSelectionColor | getDefaultNodeSelectionColor |
| getDirectlyModifiableVisualProperties | getDirectlyModifiableVisualProperties |
| getEdgeAttribute | getEdgeAttribute |
| getEdgeAttributeNames | getEdgeAttributeNames |
| getEdgeCount | getEdgeCount |
| getFirstNeighbors | getFirstNeighbors |
| getGraph | getGraph |
| getGraphFromCyWindow | getGraphFromCyWindow |
| getLayoutNameMapping | getLayoutNameMapping |
| getLayoutNames | getLayoutNames |
| getLayoutPropertyNames | getLayoutPropertyNames |
| getLayoutPropertyType | getLayoutPropertyType |
| getLayoutPropertyValue | getLayoutPropertyValue |
| getLineStyles | getLineStyles |
| getNodeAttribute | getNodeAttribute |
| getNodeAttributeNames | getNodeAttributeNames |
| getNodeCount | getNodeCount |
| getNodePosition | getNodePosition |
| getNodeShapes | getNodeShapes |
| getNodeSize | getNodeSize |
| getSelectedEdgeCount | getSelectedEdgeCount |
| getSelectedEdges | getSelectedEdges |
| getSelectedNodeCount | getSelectedNodeCount |
| getSelectedNodes | getSelectedNodes |
| getViewCoordinates | getViewCoordinates |
| getVisualStyleNames | getVisualStyleNames |
| getWindowCount | getWindowCount |
| getWindowID | getWindowID |
| getWindowList | getWindowList |
| getZoom | getZoom |
| hideAllPanels | hideAllPanels |
| hideNodes | hideNodes |
| hidePanel | hidePanel |
| hideSelectedEdges | hideSelectedEdges |
| hideSelectedNodes | hideSelectedNodes |
| initEdgeAttribute | initEdgeAttribute |
| initNodeAttribute | initNodeAttribute |
| invertEdgeSelection | invertEdgeSelection |
| invertNodeSelection | invertNodeSelection |
| layoutNetwork | layoutNetwork |
| lockNodeDimensions | lockNodeDimensions |
| makeRandomGraph | makeRandomGraph |
| makeSimpleGraph | makeSimpleGraph |
| noa | noa |
| noa.names | noa.names |
| ping | ping |
| pluginVersion | pluginVersion |
| predictTimeToDisplayGraph | predictTimeToDisplayGraph |
| raiseWindow | raiseWindow |
| RCy3 | RCy3: Display and manipulate graphs in Cytoscape >= 3.3.0 |
| redraw | redraw |
| renameCytoscapeNetwork | Rename a network |
| restoreLayout | restoreLayout |
| saveImage | saveImage |
| saveLayout | saveLayout |
| saveNetwork | saveNetwork |
| selectAllEdges | Select all edges |
| selectAllNodes | Select all nodes |
| selectEdges | selectEdges |
| selectEdgesConnectedBySelectedNodes | Select the edges connecting selected nodes in Cytoscape... |
| selectFirstNeighborsOfSelectedNodes | selectFirstNeighborsOfSelectedNodes |
| selectNodes | selectNodes |
| sendEdges | sendEdges |
| sendNodes | sendNodes |
| setCenter | setCenter |
| setCommandProperties | Runs a Cytoscape command (for example from a plugin) with a... |
| setDefaultBackgroundColor | setDefaultBackgroundColor |
| setDefaultEdgeColor | setDefaultEdgeColor |
| setDefaultEdgeFontSize | setDefaultEdgeFontSize |
| setDefaultEdgeLineStyle | setDefaultEdgeLineStyle |
| setDefaultEdgeLineWidth | setDefaultEdgeLineWidth |
| setDefaultEdgeReverseSelectionColor | setDefaultEdgeReverseSelectionColor |
| setDefaultEdgeSelectionColor | setDefaultEdgeSelectionColor |
| setDefaultEdgeSourceArrowColor | setDefaultEdgeSourceArrowColor |
| setDefaultEdgeTargetArrowColor | setDefaultEdgeTargetArrowColor |
| setDefaultNodeBorderColor | setDefaultNodeBorderColor |
| setDefaultNodeBorderWidth | setDefaultNodeBorderWidth |
| setDefaultNodeColor | setDefaultNodeColor |
| setDefaultNodeFontSize | setDefaultNodeFontSize |
| setDefaultNodeLabelColor | setDefaultNodeLabelColor |
| setDefaultNodeReverseSelectionColor | setDefaultNodeReverseSelectionColor |
| setDefaultNodeSelectionColor | setDefaultNodeSelectionColor |
| setDefaultNodeShape | setDefaultNodeShape |
| setDefaultNodeSize | setDefaultNodeSize |
| setEdgeAttributes | setEdgeAttributes |
| setEdgeAttributesDirect | setEdgeAttributesDirect |
| setEdgeColorDirect | setEdgeColorDirect |
| setEdgeColorRule | setEdgeColorRule |
| setEdgeFontSizeDirect | setEdgeFontSizeDirect |
| setEdgeLabelColorDirect | setEdgeLabelColorDirect |
| setEdgeLabelDirect | setEdgeLabelDirect |
| setEdgeLabelOpacityDirect | setEdgeLabelOpacityDirect |
| setEdgeLabelRule | setEdgeLabelRule |
| setEdgeLineStyleDirect | setEdgeLineStyleDirect |
| setEdgeLineStyleRule | specify the line styles to be used in drawing edges |
| setEdgeLineWidthDirect | setEdgeLineWidthDirect |
| setEdgeLineWidthRule | setEdgeLineWidthRule |
| setEdgeOpacityDirect | setEdgeOpacityDirect |
| setEdgeOpacityRule | setEdgeOpacityRule |
| setEdgeSourceArrowColorDirect | setEdgeSourceArrowColorDirect |
| setEdgeSourceArrowColorRule | Specify Rule for the Source Arrow Color |
| setEdgeSourceArrowOpacityDirect | setEdgeSourceArrowOpacityDirect |
| setEdgeSourceArrowRule | specify the arrow types to be used at the end of an edge at... |
| setEdgeSourceArrowShapeDirect | setEdgeSourceArrowShapeDirect |
| setEdgeTargetArrowColorDirect | setEdgeTargetArrowColorDirect |
| setEdgeTargetArrowColorRule | Specify rule for the target arrow color |
| setEdgeTargetArrowOpacityDirect | setEdgeTargetArrowOpacityDirect |
| setEdgeTargetArrowRule | specify the arrow types to be used at the end of an edge, at... |
| setEdgeTargetArrowShapeDirect | setEdgeTargetArrowShapeDirect |
| setEdgeTooltipDirect | setEdgeTooltipDirect |
| setEdgeTooltipRule | setEdgeTooltipRule |
| setGraph | setGraph |
| setLayoutProperties | setLayoutProperties |
| setNodeAttributes | setNodeAttributes |
| setNodeAttributesDirect | setNodeAttributesDirect |
| setNodeBorderColorDirect | setNodeBorderColorDirect |
| setNodeBorderColorRule | setNodeBorderColorRule |
| setNodeBorderOpacityDirect | setNodeBorderOpacityDirect |
| setNodeBorderWidthDirect | setNodeBorderWidthDirect |
| setNodeBorderWidthRule | setNodeBorderWidthRule |
| setNodeColorDirect | setNodeColorDirect |
| setNodeColorRule | setNodeColorRule |
| setNodeFillOpacityDirect | setNodeFillOpacityDirect |
| setNodeFontSizeDirect | setNodeFontSizeDirect |
| setNodeHeightDirect | setNodeHeightDirect |
| setNodeImageDirect | setNodeImageDirect |
| setNodeLabelColorDirect | setNodeLabelColorDirect |
| setNodeLabelDirect | setNodeLabelDirect |
| setNodeLabelOpacityDirect | setNodeLabelOpacityDirect |
| setNodeLabelRule | setNodeLabelRule |
| setNodeOpacityDirect | setNodeOpacityDirect |
| setNodeOpacityRule | setNodeOpacityRule |
| setNodePosition | setNodePosition |
| setNodeShapeDirect | setNodeShapeDirect |
| setNodeShapeRule | setNodeShapeRule |
| setNodeSizeDirect | setNodeSizeDirect |
| setNodeSizeRule | setNodeSizeRule |
| setNodeTooltipRule | setNodeTooltipRule |
| setNodeWidthDirect | setNodeWidthDirect |
| setTooltipDismissDelay | setTooltipDismissDelay |
| setTooltipInitialDelay | setTooltipInitialDelay |
| setVisualStyle | setVisualStyle |
| setWindowSize | setWindowSize |
| setZoom | setZoom |
| showGraphicsDetails | showGraphicsDetails |
| unhideAll | unhideAll |
