RCyjs(portRange, host="localhost", title="RCyjs", graph=graphNEL(), hideEdges=FALSE, quiet=TRUE)
simpleDemoGraph()
createTestGraph(nodeCount, edgeCount)
biocGraphToCytoscapeJSON(graph)
noa(graph, node.attribute.name)
eda(graph, edge.attribute.name)
noaNames(graph)
edaNames(graph)
"setGraph"(obj, graph, hideEdges)
"addGraph"(obj, graph)
"httpAddGraph"(obj, graph)
"httpSetStyle"(obj, filename)
"setNodeAttributes"(obj, attribute, nodes, values)
"getNodeCount"(obj)
"getEdgeCount"(obj)
"getNodes"(obj)
"getSelectedNodes"(obj)
"invertNodeSelection"(obj)
"hideSelectedNodes"(obj)
"deleteSelectedNodes"(obj)
"clearSelection"(obj)
"redraw"(obj)
"hideAllEdges"(obj)
"hideEdges"(obj, edgeType)
"showAllEdges"(obj)
"showEdges"(obj, edgeType)
"setNodeLabelRule"(obj, attribute)
"setNodeLabelAlignment"(obj, horizontal, vertical)
"setNodeSizeRule"(obj, attribute, control.points, node.sizes)
"setNodeColorRule"(obj, attribute, control.points, colors, mode)
"setNodeShapeRule"(obj, attribute, control.points, node.shapes)
"setEdgeStyle"(obj, mode)
"setEdgeColorRule"(obj, attribute, control.points, colors, mode)
"setEdgeWidthRule"(obj, attribute, control.points, widths, mode)
"setEdgeTargetArrowShapeRule"(obj, attribute, control.points, shapes)
"setEdgeTargetArrowColorRule"(obj, attribute, control.points, colors, mode)
"setEdgeSourceArrowShapeRule"(obj, attribute, control.points, shapes)
"setEdgeSourceArrowColorRule"(obj, attribute, control.points, colors, mode)
"layout"(obj, strategy)
"layoutStrategies"(obj)
"getPosition"(obj, nodeIDs=NA)
"setPosition"(obj, tbl.pos)
"getLayout"(obj)
"saveLayout"(obj, filename)
"restoreLayout"(obj, filename)
"getJSON"(obj)
"setZoom"(obj, newValue)
"getZoom"(obj)
"setBackgroundColor"(obj, newValue)
"fit"(obj, padding)
"fitContent"(obj, padding)
"fitSelectedContent"(obj, padding)
"hAlign"(obj)
"vAlign"(obj)
"layoutSelectionInGrid"(obj, x, y, w, h)
"layoutSelectionInGridInferAnchor"(obj, w, h)
"selectNodes"(obj, nodeIDs)
"sfn"(obj)
"setDefaultNodeSize"(obj, newValue)
"setDefaultNodeHeight"(obj, newValue)
"setDefaultNodeShape"(obj, newValue)
"setDefaultNodeFontSize"(obj, newValue)
"setDefaultNodeBorderColor"(obj, newValue)
"setDefaultEdgeTargetArrowShape"(obj, newValue)
"setDefaultEdgeColor"(obj, newValue)
"setDefaultEdgeTargetArrowColor"(obj, newValue)
"setDefaultEdgeFontSize"(obj, newValue)
"setDefaultEdgeWidth"(obj, newValue)
"setDefaultEdgeLineColor"(obj, newValue)
"setDefaultEdgeFont"(obj, newValue)
"setDefaultEdgeFontWeight"(obj, newValue)
"setDefaultEdgeTextOpacity"(obj, newValue)
"setDefaultEdgeLineStyle"(obj, newValue)
"setDefaultEdgeOpacity"(obj, newValue)
"setDefaultEdgeSourceArrowColor"(obj, newValue)
"setDefaultEdgeSourceArrowShape"(obj, newValue)