Upgrading Existing Scripts

The major version change from RCy3 1.x.x to 2.x.x involves a major conceptual change in translating Cytoscape into R via CyREST. This allows for easier R script writing and package maintenance. Unfortunately, this also means that existing scripts written against older versions of RCy3 will not work and the upgrade can not be automated.

Here are some tips for upgrading existing scripts to work with RCy3 2.0.0 and greater.

1. CytosacpeConnection and CytoscapeWindow classes are no longer used.
   • You can delete all references to CytoscapeConnection and cc variables.
   • In some cases, you can replace references to CytoscapeWindow with createNetworkFromGraph, which returns a network SUID (rather than an R object). In general, you can either swap in network SUIDs for CytoscapeWindow or cw variables. And in most cases where you are dealing with the current network (i.e., currently selected network in Cytoscape), you can simply delete cw from your code.
2. Most functions containing "Window" in their name have been renamed to "Network". E.g., getWindowList -> getNetworkList and deleteWindow -> deleteNetwork. Most of these have been deprecated so they will work for a while longer, but will eventually be removed from the package and should be updated.
3. Visual style setting methods have been updated to more consistently match Cytoscape's terminology.
   • All "Direct" methods (e.g., setNodeShapeDirect) have been renamed "Bypass" (e.g., setNodeShapeBypass).
   • All "Default" methods (e.g., setDefaultNodeShape) have been renamed like setNodeShapeDefault.
   • All "Rule" methods (e.g., setNodeShapeRule) have been renamed to "Mappings" (e.g., setNodeShapeMapping).
4. All the graphNEL-specific functions are now defunct. Since you no longer need to manage a CytoscapeWindow, you no longer use functions like sendNodes, sendNodeAttribute, addGraphToGraph. Instead, these functions will need to be replaced with createNetwork... functions and loadTableData.
5. The functions for get/setNodePositions and save/restoreLayout have been replaced with a single layoutCopycat function.
6. The redraw function is no longer needed. In order to set a layout, you can simply use setVisualStyle.

Table of renamed and replaced functions

old function	new function	comments
createWindow	createNetworkFromGraph	returns network SUID rather than an object
createWindowFromSelection	createSubnetwork("selected")
copyCytoscapeNetwork	cloneNetwork
CytoscapeWindow	createNetworkFromGraph	returns network SUID rather than an object
deleteAllWindows	deleteAllNetworks
deleteWindow	deleteNetwork
deleteEdgeAttribute	deleteTableColumn(attribute.name,'edge')
deleteNodeAttribute	deleteTableColumn(attribute.name,'node')
existing.CytoscapeWindow	getNetworkSuid
fitSelectedContent	fitContent(selected.only = TRUE)
getAllNodeAttributes	getTableColumns()
getAllEdgeAttributes	getTableColumns('edge')
getCenter	getNetworkCenter
getCommandNames	commandsHelp
getCommandsWithinNamespace	commandsHelp(namespace)
getDirectlyModifiableVisualProperties	getVisualPropertyNames
getEdgeAttribute	getTableValue('edge',edge.name, attribute.name)
getEdgeAttributeNames	getTableColumnNames('edge')
getGraphFromCyWindow	createGraphFromNetwork
getNodeAttribute	getTableValue('node',node.name, attribute.name)
getNodeAttributeNames	getTableColumnNames('node')
getNodePositions	getNodePosition
getWindowCount	getNetworkCount
getWindowID	getNetworkSuid
getWindowList	getNetworkList
getZoom	getNetworkZoom
ping	cytoscapePing
pluginVersion	cytoscapeVersionInfo	the new function offers additional info
renameCytoscapeNetwork	renameNetwork
saveImage	exportImage
save/restoreLayout	layoutCopyCat
saveNetwork	saveSession
selectEdgesConnectedBySelectedNodes	selectEdgesConnectingSelectedNodes
selectFirstNeighborsOfSelectedNodes	selectFirstNeighbors
setCenter	setNetworkCenterBypass
setNodePositions	setNodePropertyBypass	NODE_X_LOCATION, NODE_Y_LOCATION
setDefault...	set...Default
set...Direct	set...Bypass	bug fixed: bypasses are now persistent
set...Rule	set...Mapping
setZoom	setNetworkZoomBypass
sfn	selectFirstNeighbors
showGraphicsDetails	toggleGraphicsDetails

Table of defunct functions no longer supported

defunct function	comments
addCyEdge
addCyNode
addGraphToGraph
connectToNewestCyWindow
cy2.edge.names
cyPlot
demoSimpleGraph	see makeSimpleGraph
displayGraph	see createNetworkFromGraph
eda
eda.names
getAdjacentEdgeNames	use selectNodes, selectEdgesAdjacentToSelectedNodes
getAttributeClassNames
getDefaultEdgeReverseSelectionColor	no longer exists in Cytoscape
getDefaultNodeReverseSelectionColor	no longer exists in Cytoscape
getGraph	see createGraphFromNetwork
getNodePosition	see getNodeProperty
getViewCoordinates
initEdgeAttribute
initNodeAttribute
makeRandomGraph	see makeSimpleGraph
noa
noa.names
predictTimeToDisplayGraph
raiseWindow
sendEdges
sendNodes
setCommandProperties	see commandsRun
setDefaultEdgeReverseSelectionColor	no longer exists in Cytoscape
setDefaultNodeReverseSelectionColor	no longer exists in Cytoscape
setEdgeAttributes	see loadTableData
setGraph
setNodeAttributes	see loadTableData
setNodePosition	see setNodePropertyBypass
setTooltipDismissDelay
setTooltipInitialDelay
setWindowSize

It is just not going to work!

If this upgrade simply takes too much or effort for your needs, then you can continue to rely on the last versions of RCy3 prior to 2.0:

• archived releases at bioconductor
• archived git repo (for development)