Name Mode Size
..
AddToGroup.Rd 100644 1 kb
RCy3.Rd 100644 0 kb
RemoveFromGroup.Rd 100644 1 kb
UpdateAnnotationBoundedText.Rd 100644 3 kb
addAnnotationBoundedText.Rd 100644 3 kb
addAnnotationImage.Rd 100644 3 kb
addAnnotationShape.Rd 100644 3 kb
addAnnotationText.Rd 100644 2 kb
addCyEdges.Rd 100644 1 kb
addCyNodes.Rd 100644 1 kb
analyzeNetwork.Rd 100644 1 kb
applyFilter.Rd 100644 1 kb
bundleEdges.Rd 100644 1 kb
checkNotebookIsRunning.Rd 100644 0 kb
checkRunningRemote.Rd 100644 1 kb
clearEdgeBends.Rd 100644 1 kb
clearEdgePropertyBypass.Rd 100644 1 kb
clearNetworkCenterBypass.Rd 100644 1 kb
clearNetworkPropertyBypass.Rd 100644 1 kb
clearNetworkZoomBypass.Rd 100644 1 kb
clearNodeOpacityBypass.Rd 100644 1 kb
clearNodePropertyBypass.Rd 100644 1 kb
clearSelection.Rd 100644 1 kb
cloneNetwork.Rd 100644 1 kb
closeSession.Rd 100644 1 kb
collapseGroup.Rd 100644 1 kb
commandEcho.Rd 100644 1 kb
commandOpenDialog.Rd 100644 1 kb
commandPause.Rd 100644 1 kb
commandQuit.Rd 100644 1 kb
commandRunFile.Rd 100644 1 kb
commandSleep.Rd 100644 1 kb
commandsAPI.Rd 100644 1 kb
commandsGET.Rd 100644 1 kb
commandsHelp.Rd 100644 1 kb
commandsPOST.Rd 100644 1 kb
commandsRun.Rd 100644 1 kb
copyVisualStyle.Rd 100644 1 kb
createColumnFilter.Rd 100644 3 kb
createCompositeFilter.Rd 100644 2 kb
createCytoscapejsFromNetwork.Rd 100644 1 kb
createDegreeFilter.Rd 100644 2 kb
createGraphFromNetwork.Rd 100644 1 kb
createGroup.Rd 100644 1 kb
createGroupByColumn.Rd 100644 1 kb
createIgraphFromNetwork.Rd 100644 1 kb
createNetworkFromCytoscapejs.Rd 100644 1 kb
createNetworkFromDataFrames.Rd 100644 3 kb
createNetworkFromGraph.Rd 100644 1 kb
createNetworkFromIgraph.Rd 100644 2 kb
createSubnetwork.Rd 100644 2 kb
createView.Rd 100644 1 kb
createVisualStyle.Rd 100644 2 kb
cybrowserClose.Rd 100644 1 kb
cybrowserDialog.Rd 100644 1 kb
cybrowserHide.Rd 100644 1 kb
cybrowserList.Rd 100644 1 kb
cybrowserSend.Rd 100644 1 kb
cybrowserShow.Rd 100644 1 kb
cybrowserVersion.Rd 100644 1 kb
cyrestAPI.Rd 100644 1 kb
cyrestDELETE.Rd 100644 1 kb
cyrestGET.Rd 100644 1 kb
cyrestPOST.Rd 100644 1 kb
cyrestPUT.Rd 100644 1 kb
cytoscapeApiVersions.Rd 100644 1 kb
cytoscapeFreeMemory.Rd 100644 1 kb
cytoscapeMemoryStatus.Rd 100644 1 kb
cytoscapeNumberOfCores.Rd 100644 1 kb
cytoscapePing.Rd 100644 1 kb
cytoscapeVersionInfo.Rd 100644 1 kb
deleteAllNetworks.Rd 100644 1 kb
deleteAllVisualStyle.Rd 100644 1 kb
deleteAnnotation.Rd 100644 1 kb
deleteDuplicateEdges.Rd 100644 1 kb
deleteGroup.Rd 100644 1 kb
deleteNetwork.Rd 100644 1 kb
deleteSelectedEdges.Rd 100644 1 kb
deleteSelectedNodes.Rd 100644 1 kb
deleteSelfLoops.Rd 100644 1 kb
deleteStyleMapping.Rd 100644 1 kb
deleteTableColumn.Rd 100644 1 kb
deleteVisualStyle.Rd 100644 1 kb
diffusionAdvanced.Rd 100644 1 kb
diffusionBasic.Rd 100644 1 kb
disableApp.Rd 100644 1 kb
doInitializeSandbox.Rd 100644 1 kb
doRequestRemote.Rd 100644 1 kb
doSetSandbox.Rd 100644 1 kb
dockPanel.Rd 100644 1 kb
dot-exportShowImage.Rd 100644 3 kb
dot-getDefaultSandbox.Rd 100644 0 kb
dot-getRequester.Rd 100644 0 kb
enableApp.Rd 100644 1 kb
expandGroup.Rd 100644 1 kb
exportFilters.Rd 100644 1 kb
exportImage.Rd 100644 2 kb
exportJPG.Rd 100644 2 kb
exportNetwork.Rd 100644 1 kb
exportNetworkToNDEx.Rd 100644 1 kb
exportPDF.Rd 100644 2 kb
exportPNG.Rd 100644 2 kb
exportPS.Rd 100644 2 kb
exportSVG.Rd 100644 2 kb
exportVisualStyles.Rd 100644 2 kb
findRemoteCytoscape.Rd 100644 0 kb
fitContent.Rd 100644 1 kb
floatPanel.Rd 100644 1 kb
getAbsSandboxPath.Rd 100644 0 kb
getAllEdges.Rd 100644 1 kb
getAllNodes.Rd 100644 1 kb
getAllStyleMappings.Rd 100644 1 kb
getAnnotationList.Rd 100644 1 kb
getAppInformation.Rd 100644 1 kb
getAppStatus.Rd 100644 1 kb
getAppUpdates.Rd 100644 1 kb
getArrowShapes.Rd 100644 1 kb
getAvailableApps.Rd 100644 1 kb
getBackgroundColorDefault.Rd 100644 1 kb
getBrowserClientChannel.Rd 100644 0 kb
getBrowserClientJs.Rd 100644 0 kb
getCollectionList.Rd 100644 1 kb
getCollectionName.Rd 100644 1 kb
getCollectionNetworks.Rd 100644 1 kb
getCollectionSuid.Rd 100644 1 kb
getCurrentSandbox.Rd 100644 0 kb
getCurrentSandboxName.Rd 100644 0 kb
getCurrentSandboxPath.Rd 100644 0 kb
getCurrentStyle.Rd 100644 1 kb
getDefaultSandbox.Rd 100644 0 kb
getDefaultSandboxPath.Rd 100644 0 kb
getDisabledApps.Rd 100644 1 kb
getEdgeColor.Rd 100644 1 kb
getEdgeCount.Rd 100644 1 kb
getEdgeInfo.Rd 100644 1 kb
getEdgeLineStyle.Rd 100644 1 kb
getEdgeLineWidth.Rd 100644 1 kb
getEdgeProperty.Rd 100644 1 kb
getEdgeSelectionColorDefault.Rd 100644 1 kb
getEdgeTargetArrowShape.Rd 100644 1 kb
getFilterList.Rd 100644 1 kb
getFirstNeighbors.Rd 100644 1 kb
getGroupInfo.Rd 100644 1 kb
getInstalledApps.Rd 100644 1 kb
getJupyterBridgeURL.Rd 100644 0 kb
getLayoutNameMapping.Rd 100644 1 kb
getLayoutNames.Rd 100644 1 kb
getLayoutPropertyNames.Rd 100644 1 kb
getLayoutPropertyType.Rd 100644 1 kb
getLayoutPropertyValue.Rd 100644 1 kb
getLineStyles.Rd 100644 1 kb
getNetworkCenter.Rd 100644 1 kb
getNetworkCount.Rd 100644 1 kb
getNetworkList.Rd 100644 1 kb
getNetworkNDExId.Rd 100644 1 kb
getNetworkName.Rd 100644 1 kb
getNetworkProperty.Rd 100644 1 kb
getNetworkSuid.Rd 100644 1 kb
getNetworkViewSuid.Rd 100644 1 kb
getNetworkViews.Rd 100644 1 kb
getNetworkZoom.Rd 100644 1 kb
getNodeColor.Rd 100644 1 kb
getNodeCount.Rd 100644 1 kb
getNodeHeight.Rd 100644 1 kb
getNodePosition.Rd 100644 1 kb
getNodeProperty.Rd 100644 1 kb
getNodeSelectionColorDefault.Rd 100644 1 kb
getNodeShapes.Rd 100644 1 kb
getNodeSize.Rd 100644 1 kb
getNodeWidth.Rd 100644 1 kb
getNotebookIsRunning.Rd 100644 0 kb
getSandboxReinitialize.Rd 100644 0 kb
getSelectedEdgeCount.Rd 100644 1 kb
getSelectedEdges.Rd 100644 1 kb
getSelectedNodeCount.Rd 100644 1 kb
getSelectedNodes.Rd 100644 1 kb
getStyleDependencies.Rd 100644 1 kb
getStyleMapping.Rd 100644 1 kb
getTableColumnNames.Rd 100644 1 kb
getTableColumnTypes.Rd 100644 1 kb
getTableColumns.Rd 100644 1 kb
getTableValue.Rd 100644 1 kb
getUninstalledApps.Rd 100644 1 kb
getVisualPropertyDefault.Rd 100644 1 kb
getVisualPropertyNames.Rd 100644 1 kb
getVisualStyleJSON.Rd 100644 1 kb
getVisualStyleNames.Rd 100644 1 kb
groupAnnotation.Rd 100644 1 kb
hideAllPanels.Rd 100644 1 kb
hideEdges.Rd 100644 1 kb
hideNodes.Rd 100644 1 kb
hidePanel.Rd 100644 1 kb
hideSelectedEdges.Rd 100644 1 kb
hideSelectedNodes.Rd 100644 1 kb
importFileFromUrl.Rd 100644 3 kb
importFilters.Rd 100644 1 kb
importNetworkFromFile.Rd 100644 1 kb
importNetworkFromNDEx.Rd 100644 1 kb
importVisualStyles.Rd 100644 1 kb
installApp.Rd 100644 1 kb
invertEdgeSelection.Rd 100644 1 kb
invertNodeSelection.Rd 100644 1 kb
layoutCopycat.Rd 100644 2 kb
layoutNetwork.Rd 100644 1 kb
listGroups.Rd 100644 1 kb
loadTableData.Rd 100644 2 kb
lockNodeDimensions.Rd 100644 1 kb
makeSimpleGraph.Rd 100644 1 kb
makeSimpleIgraph.Rd 100644 1 kb
mapTableColumn.Rd 100644 2 kb
mapVisualProperty.Rd 100644 4 kb
matchArrowColorToEdge.Rd 100644 1 kb
mergeNetworks.Rd 100644 3 kb
notebookExportShowImage.Rd 100644 2 kb
notebookShowImage.Rd 100644 2 kb
openAppStore.Rd 100644 1 kb
openSession.Rd 100644 1 kb
paletteColorBrewerAccent.Rd 100644 1 kb
paletteColorBrewerBlues.Rd 100644 1 kb
paletteColorBrewerBrBG.Rd 100644 1 kb
paletteColorBrewerBuGn.Rd 100644 1 kb
paletteColorBrewerBuPu.Rd 100644 1 kb
paletteColorBrewerDark2.Rd 100644 1 kb
paletteColorBrewerGnBu.Rd 100644 1 kb
paletteColorBrewerGreens.Rd 100644 1 kb
paletteColorBrewerGreys.Rd 100644 1 kb
paletteColorBrewerOrRd.Rd 100644 1 kb
paletteColorBrewerOranges.Rd 100644 1 kb
paletteColorBrewerPRGn.Rd 100644 1 kb
paletteColorBrewerPaired.Rd 100644 1 kb
paletteColorBrewerPastel1.Rd 100644 1 kb
paletteColorBrewerPastel2.Rd 100644 1 kb
paletteColorBrewerPiYG.Rd 100644 1 kb
paletteColorBrewerPuBu.Rd 100644 1 kb
paletteColorBrewerPuBuGn.Rd 100644 1 kb
paletteColorBrewerPuOr.Rd 100644 1 kb
paletteColorBrewerPuRd.Rd 100644 1 kb
paletteColorBrewerPurples.Rd 100644 1 kb
paletteColorBrewerRdBu.Rd 100644 1 kb
paletteColorBrewerRdPu.Rd 100644 1 kb
paletteColorBrewerRdYlBu.Rd 100644 1 kb
paletteColorBrewerReds.Rd 100644 1 kb
paletteColorBrewerSet1.Rd 100644 1 kb
paletteColorBrewerSet2.Rd 100644 1 kb
paletteColorBrewerSet3.Rd 100644 1 kb
paletteColorBrewerYlGn.Rd 100644 1 kb
paletteColorBrewerYlGnBu.Rd 100644 1 kb
paletteColorBrewerYlOrBr.Rd 100644 1 kb
paletteColorBrewerYlOrRd.Rd 100644 1 kb
paletteColorRandom.Rd 100644 0 kb
removeNodeCustomGraphics.Rd 100644 1 kb
renameNetwork.Rd 100644 1 kb
renameTableColumn.Rd 100644 1 kb
resetDefaultSandbox.Rd 100644 0 kb
runningRemoteCheck.Rd 100644 0 kb
sandboxGetFileInfo.Rd 100644 2 kb
sandboxGetFrom.Rd 100644 1 kb
sandboxInitializer.Rd 100644 0 kb
sandboxRemove.Rd 100644 1 kb
sandboxRemoveFile.Rd 100644 1 kb
sandboxSendTo.Rd 100644 2 kb
sandboxSet.Rd 100644 2 kb
sandboxUrlTo.Rd 100644 1 kb
saveSession.Rd 100644 1 kb
selectAll.Rd 100644 1 kb
selectAllEdges.Rd 100644 1 kb
selectAllNodes.Rd 100644 1 kb
selectEdges.Rd 100644 1 kb
selectEdgesAdjacentToNodes.Rd 100644 1 kb
selectEdgesAdjacentToSelectedNodes.Rd 100644 1 kb
selectEdgesConnectingSelectedNodes.Rd 100644 1 kb
selectFirstNeighbors.Rd 100644 1 kb
selectNodes.Rd 100644 1 kb
selectNodesConnectedBySelectedEdges.Rd 100644 1 kb
setBackgroundColorDefault.Rd 100644 1 kb
setCatchupFilterSecs.Rd 100644 1 kb
setCatchupNetworkSecs.Rd 100644 1 kb
setCurrentNetwork.Rd 100644 1 kb
setCurrentSandbox.Rd 100644 0 kb
setCurrentView.Rd 100644 1 kb
setDefaultSandbox.Rd 100644 0 kb
setDefaultSandboxPath.Rd 100644 0 kb
setEdgeColorBypass.Rd 100644 1 kb
setEdgeColorDefault.Rd 100644 1 kb
setEdgeColorMapping.Rd 100644 2 kb
setEdgeFontFaceBypass.Rd 100644 1 kb
setEdgeFontFaceDefault.Rd 100644 1 kb
setEdgeFontFaceMapping.Rd 100644 1 kb
setEdgeFontSizeBypass.Rd 100644 1 kb
setEdgeFontSizeDefault.Rd 100644 1 kb
setEdgeFontSizeMapping.Rd 100644 2 kb
setEdgeLabelBypass.Rd 100644 1 kb
setEdgeLabelColorBypass.Rd 100644 1 kb
setEdgeLabelColorDefault.Rd 100644 1 kb
setEdgeLabelColorMapping.Rd 100644 2 kb
setEdgeLabelDefault.Rd 100644 1 kb
setEdgeLabelMapping.Rd 100644 1 kb
setEdgeLabelOpacityBypass.Rd 100644 1 kb
setEdgeLabelOpacityDefault.Rd 100644 1 kb
setEdgeLabelOpacityMapping.Rd 100644 2 kb
setEdgeLineStyleBypass.Rd 100644 1 kb
setEdgeLineStyleDefault.Rd 100644 1 kb
setEdgeLineStyleMapping.Rd 100644 1 kb
setEdgeLineWidthBypass.Rd 100644 1 kb
setEdgeLineWidthDefault.Rd 100644 1 kb
setEdgeLineWidthMapping.Rd 100644 2 kb
setEdgeOpacityBypass.Rd 100644 1 kb
setEdgeOpacityDefault.Rd 100644 1 kb
setEdgeOpacityMapping.Rd 100644 2 kb
setEdgePropertyBypass.Rd 100644 1 kb
setEdgeSelectionColorDefault.Rd 100644 1 kb
setEdgeSourceArrowColorBypass.Rd 100644 1 kb
setEdgeSourceArrowColorDefault.Rd 100644 1 kb
setEdgeSourceArrowColorMapping.Rd 100644 2 kb
setEdgeSourceArrowMapping.Rd 100644 1 kb
setEdgeSourceArrowShapeBypass.Rd 100644 1 kb
setEdgeSourceArrowShapeDefault.Rd 100644 1 kb
setEdgeSourceArrowShapeMapping.Rd 100644 2 kb
setEdgeTargetArrowColorBypass.Rd 100644 1 kb
setEdgeTargetArrowColorDefault.Rd 100644 1 kb
setEdgeTargetArrowColorMapping.Rd 100644 2 kb
setEdgeTargetArrowMapping.Rd 100644 1 kb
setEdgeTargetArrowShapeBypass.Rd 100644 1 kb
setEdgeTargetArrowShapeDefault.Rd 100644 1 kb
setEdgeTargetArrowShapeMapping.Rd 100644 2 kb
setEdgeTooltipBypass.Rd 100644 1 kb
setEdgeTooltipDefault.Rd 100644 1 kb
setEdgeTooltipMapping.Rd 100644 1 kb
setLayoutProperties.Rd 100644 1 kb
setModelPropagationSecs.Rd 100644 1 kb
setNetworkCenterBypass.Rd 100644 1 kb
setNetworkPropertyBypass.Rd 100644 1 kb
setNetworkZoomBypass.Rd 100644 1 kb
setNodeBorderColorBypass.Rd 100644 1 kb
setNodeBorderColorDefault.Rd 100644 1 kb
setNodeBorderColorMapping.Rd 100644 2 kb
setNodeBorderOpacityBypass.Rd 100644 1 kb
setNodeBorderOpacityDefault.Rd 100644 1 kb
setNodeBorderOpacityMapping.Rd 100644 2 kb
setNodeBorderWidthBypass.Rd 100644 1 kb
setNodeBorderWidthDefault.Rd 100644 1 kb
setNodeBorderWidthMapping.Rd 100644 2 kb
setNodeColorBypass.Rd 100644 1 kb
setNodeColorDefault.Rd 100644 1 kb
setNodeColorMapping.Rd 100644 2 kb
setNodeComboOpacityMapping.Rd 100644 2 kb
setNodeCustomBarChart.Rd 100644 2 kb
setNodeCustomBoxChart.Rd 100644 2 kb
setNodeCustomHeatMapChart.Rd 100644 2 kb
setNodeCustomLineChart.Rd 100644 2 kb
setNodeCustomLinearGradient.Rd 100644 1 kb
setNodeCustomPieChart.Rd 100644 1 kb
setNodeCustomPosition.Rd 100644 1 kb
setNodeCustomRadialGradient.Rd 100644 1 kb
setNodeCustomRingChart.Rd 100644 1 kb
setNodeFillOpacityBypass.Rd 100644 1 kb
setNodeFillOpacityDefault.Rd 100644 1 kb
setNodeFillOpacityMapping.Rd 100644 2 kb
setNodeFontFaceBypass.Rd 100644 1 kb
setNodeFontFaceDefault.Rd 100644 1 kb
setNodeFontFaceMapping.Rd 100644 1 kb
setNodeFontSizeBypass.Rd 100644 1 kb
setNodeFontSizeDefault.Rd 100644 1 kb
setNodeFontSizeMapping.Rd 100644 2 kb
setNodeHeightBypass.Rd 100644 1 kb
setNodeHeightDefault.Rd 100644 1 kb
setNodeHeightMapping.Rd 100644 2 kb
setNodeLabelBypass.Rd 100644 1 kb
setNodeLabelColorBypass.Rd 100644 1 kb
setNodeLabelColorDefault.Rd 100644 1 kb
setNodeLabelColorMapping.Rd 100644 2 kb
setNodeLabelDefault.Rd 100644 1 kb
setNodeLabelMapping.Rd 100644 1 kb
setNodeLabelOpacityBypass.Rd 100644 1 kb
setNodeLabelOpacityDefault.Rd 100644 1 kb
setNodeLabelOpacityMapping.Rd 100644 2 kb
setNodeOpacityBypass.Rd 100644 1 kb
setNodePropertyBypass.Rd 100644 1 kb
setNodeSelectionColorDefault.Rd 100644 1 kb
setNodeShapeBypass.Rd 100644 1 kb
setNodeShapeDefault.Rd 100644 1 kb
setNodeShapeMapping.Rd 100644 1 kb
setNodeSizeBypass.Rd 100644 1 kb
setNodeSizeDefault.Rd 100644 1 kb
setNodeSizeMapping.Rd 100644 2 kb
setNodeTooltipBypass.Rd 100644 1 kb
setNodeTooltipDefault.Rd 100644 1 kb
setNodeTooltipMapping.Rd 100644 1 kb
setNodeWidthBypass.Rd 100644 1 kb
setNodeWidthDefault.Rd 100644 1 kb
setNodeWidthMapping.Rd 100644 2 kb
setNotebookIsRunning.Rd 100644 0 kb
setSandboxReinitialize.Rd 100644 0 kb
setStyleDependencies.Rd 100644 1 kb
setVisualPropertyDefault.Rd 100644 1 kb
setVisualStyle.Rd 100644 1 kb
spoofResponse-class.Rd 100644 0 kb
syncNodeCustomGraphicsSize.Rd 100644 1 kb
toggleGraphicsDetails.Rd 100644 1 kb
ungroupAnnotation.Rd 100644 1 kb
unhideAll.Rd 100644 1 kb
unhideEdges.Rd 100644 1 kb
unhideNodes.Rd 100644 1 kb
uninstallApp.Rd 100644 1 kb
updateAnnotationImage.Rd 100644 3 kb
updateAnnotationShape.Rd 100644 3 kb
updateAnnotationText.Rd 100644 2 kb
updateApp.Rd 100644 1 kb
updateGroupAnnotation.Rd 100644 2 kb
updateNetworkInNDEx.Rd 100644 1 kb
updateStyleDefaults.Rd 100644 1 kb
updateStyleMapping.Rd 100644 1 kb
README.md
# Welcome to RCy3: 2.0 and Beyond [![BioC Release Build Status](http://bioconductor.org/shields/build/release/bioc/RCy3.svg)](http://bioconductor.org/checkResults/release/bioc-LATEST/RCy3/) - Bioconductor Release Build [![BioC Dev Build Status](http://bioconductor.org/shields/build/devel/bioc/RCy3.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/RCy3/) - Bioconductor Dev Build [![Travis-CI Build Status](https://travis-ci.org/cytoscape/RCy3.svg?branch=master)](https://travis-ci.org/cytoscape/RCy3) - GitHub Dev Build by Travis Building upon the phenominal success of RCytoscape and RCy3, Cytoscape is adopting this project to provide a robust R package for the rapidly evolving Cytoscape ecosystem. We are beginning with a major refactor of RCy3 that includes: * independence from the graphNEL object model * harmonized function and argument names * support for Cytoscape commands * better support for Cytoscape apps * see [NEWS](https://github.com/cytoscape/RCy3/blob/master/NEWS) for the complete release notes * coordinated development with CyREST and the Cytoscape service model * [New API](https://github.com/cytoscape/cyREST/issues?utf8=✓&q=milestone%3A*+label%3A%22new+API%22+is%3A*) * coordinated development with other scripting libraries, e.g., * [py4cytoscape](https://github.com/cytoscape/py4cytoscape) * [RCyjs](http://bioconductor.org/packages/release/bioc/html/RCyjs.html) ## Getting Started * [Documenation site](http://cytoscape.org/RCy3/index.html) * [Cytoscape Rmd noteboods](https://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/) ## How to install **_Official bioconductor releases_ (recommended)** ``` install.packages("BiocManager") BiocManager::install("RCy3") ``` *Note: Be sure to use the [latest Bioconductor](https://www.bioconductor.org/install/) and recommended R version* **_Development version from this repo_ (at your own risk)** ``` install.packages("devtools") library(devtools) install_github('cytoscape/RCy3', build_vignettes=FALSE) #If installation fails due to package 'XXX' not found, # then run install.packages("XXX") and then try install_github('cytoscape/RCy3') again library(RCy3) ``` #### Troubleshooting 1. If you see this error on a Mac: ```make: gfortran-4.8: No such file or directory```, then try reinstalling R via [homebrew](https://brew.sh/): ```brew update && brew reinstall r``` * warning: this may take ~30 minutes 2. If you see this error in RStudio: ```ERROR: dependency ‘XML’ is not available for package```, then try this command: ```install.packages("XML")``` and then try installing RCy3 again. ## How to contribute This is a public, open source project. Come on in! You can contribute at multiple levels: * Report an issue or feature request * Fork and make pull requests * Contact current Cytoscape developers and inquire about joining the team ### Development ``` install.packages("devtools") install.packages("roxygen2") library(devtools,roxygen2) devtools::install_github("AlexanderPico/docthis") library(docthis) #shift+cmd+D BiocManager::install("BiocStyle") library(BiocStyle) BiocManager::install("BiocCheck") library(BiocCheck) install.packages("RUnit") library(RUnit) setwd("/git/cytoscape/RCy3") #customize to your setup devtools::document() devtools::check(args = "--no-examples", vignettes = F) BiocCheck::BiocCheck('./') ``` ### Testing Unit tests are a crucial tool in software development. In order to run them 'offline' (not on the Bioconductor build system), take these steps from within a running R session (requires RUnit): ``` source(system.file("unitTests", "test_RCy3.R", package="RCy3")) run.tests() ``` They take about 4 minutes to run. ### Updating site We use [pkgdown](https://pkgdown.r-lib.org/) to generate the [main site for RCy3](http://cytoscape.org/RCy3/index.html) based on this README, metadata, man pages and vignettes. If you make changes to any of these, please take a moment to regenerate the site: ``` library(pkgdown) pkgdown::build_site(examples=FALSE) ``` ### Bioconductor While this is the primary development repository for the RCy3 project, we also make regular pushes to official bioconductor repository ([devel](http://bioconductor.org/packages/devel/bioc/html/RCy3.html) & [release](http://bioconductor.org/packages/release/bioc/html/RCy3.html)) from which the official releases are generated. This is the correct repo for all coding and bug reporting interests. The tagged releases here correspond to the bioconductor releases via a manual syncing process. The `master` branch here corresponds to the latest code in development and not yet released. ``` git commit -m "informative commit message" git push origin master git push upstream master ``` http://bioconductor.org/developers/how-to/git/push-to-github-bioc/ Following each bioconductor release, a `RELEASE_#_#` branch is created. The new branch is fetched and master is updated: ``` git fetch upstream git checkout -b RELEASE_3_13 upstream/RELEASE_3_13 git push origin RELEASE_3_13 git checkout master git pull upstream master git push origin master ``` Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to `master`, then: ``` git checkout RELEASE_3_13 git cherry-pick master #for lastest commit # or git cherry-pick 1abc234 #for specific commit # or git cherry-pick 1abc234^..5def678 #for an inclusive range # bump release version in DESCRIPTION git commit -am 'version bump' git push origin RELEASE_3_13 # double check changes, and then... git push upstream RELEASE_3_13 git checkout master # bump dev version in DESCRIPTION git commit -am 'version bump' git push origin master git push upstream master ``` https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ ### Vignettes When adding or updating vignettes, consider the following tips for consistency: * Copy/paste the header from an existing RCy3 vignette, including the global knitr options * Number the *VignetteIndexEntry* names w.r.t. other vignettes (this determines their presentation order) * Avoid spaces in Rmd filenames; causes CHECK errors * When ready, run **Knit to html_document** and review the generated html (requires BiocStyle) * Note: you don't need to save the html version; it will be generated anew at Bioconductor. * In the end, you should just have an Rmd version of each vignette in the repo. ### Former Repo The entire commit history has been preserved during this transition, but you can find the repo for RCy3 v1.5.3 and earlier at https://github.com/tmuetze/Bioconductor_RCy3_the_new_RCytoscape and you can find the Bioconductor page for v1.8.0, including archives at https://www.bioconductor.org/packages/3.6/bioc/html/RCy3.html. ```Note to repository maintainers: Please *DO NOT* move this page ... the Cytoscape Automation paper refers directly to it.```