Package 'RCy3'

Description

Show network view in notebook output.

Usage

.exportShowImage(
  exportFirst,
  filename = "image",
  type = "PNG",
  resolution = NULL,
  units = NULL,
  height = NULL,
  width = NULL,
  zoom = NULL,
  sandboxName = NULL,
  network = NULL,
  base.url = .defaultBaseUrl,
  overwriteFile = TRUE
)

Arguments

Details

Show network view in notebook output.

Value

display image

Examples

.exportShowImage()

Description

.getDefaultSandbox

Usage

.getDefaultSandbox(base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

.getDefaultSandbox()

Description

.getRequester

Usage

.getRequester(base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

.getRequester()

Description

Adds a bounded text annotation to a Cytoscape network view. The object will also be added to the Annotation Panel in the GUI.

Usage

addAnnotationBoundedText(
  text = NULL,
  x.pos = NULL,
  y.pos = NULL,
  fontSize = NULL,
  fontFamily = NULL,
  fontStyle = NULL,
  color = NULL,
  angle = NULL,
  type = NULL,
  customShape = NULL,
  fillColor = NULL,
  opacity = NULL,
  borderThickness = NULL,
  borderColor = NULL,
  borderOpacity = NULL,
  height = NULL,
  width = NULL,
  name = NULL,
  canvas = NULL,
  z.order = NULL,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

A named list of annotation properties, including UUID

Examples

addAnnotationBoundedText("test1")
addAnnotationBoundedText("test2", 1000, 1000, name="B2")
addAnnotationBoundedText("test3", 1200, 1000, 30, "Helvetica", "bold", "#990000",
    40,name="B3", canvas="foreground",z=4)

Description

Adds a Image annotation to a Cytoscape network view. The object will also be added to the Annotation Panel in the GUI.

Usage

addAnnotationImage(
  url = NULL,
  x.pos = NULL,
  y.pos = NULL,
  angle = NULL,
  opacity = NULL,
  brightness = NULL,
  contrast = NULL,
  borderThickness = NULL,
  borderColor = NULL,
  borderOpacity = NULL,
  height = NULL,
  width = NULL,
  name = NULL,
  canvas = NULL,
  z.order = NULL,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

A named list of annotation properties, including UUID

Examples

addAnnotationImage("image.png")
addAnnotationImage("/Users/janedoe/Desktop/image.png", 1000, 1000, name="I2")
addAnnotationImage("https://www.example.com/image.png", 1200, 1000, 30, 
    40, name="I3", canvas="background",z=4)

Description

Adds a shape annotation to a Cytoscape network view. The object will also be added to the Annotation Panel in the GUI.

Usage

addAnnotationShape(
  type = NULL,
  customShape = NULL,
  x.pos = NULL,
  y.pos = NULL,
  angle = NULL,
  fillColor = NULL,
  opacity = NULL,
  borderThickness = NULL,
  borderColor = NULL,
  borderOpacity = NULL,
  height = NULL,
  width = NULL,
  name = NULL,
  canvas = NULL,
  z.order = NULL,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

A named list of annotation properties, including UUID

Examples

addAnnotationShape("rectangle")
addAnnotationShape("rectangle", 1000, 1000, name="S2")
addAnnotationShape("rectangle", 1200, 1000, 30, "#990000",
    40,name="S3", canvas="background",z=4)

Description

Adds a text annotation to a Cytoscape network view. The object will also be added to the Annotation Panel in the GUI.

Usage

addAnnotationText(
  text = NULL,
  x.pos = NULL,
  y.pos = NULL,
  fontSize = NULL,
  fontFamily = NULL,
  fontStyle = NULL,
  color = NULL,
  angle = NULL,
  name = NULL,
  canvas = NULL,
  z.order = NULL,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

A named list of annotation properties, including UUID

Examples

addAnnotationText("test1")
addAnnotationText("test2", 1000, 1000, name="T2")
addAnnotationText("test3", 1200, 1000, 30, "Helvetica", "bold", "#990000",
    40,name="T3", canvas="foreground",z=4)

Description

Add one or more edges to a Cytoscape network by listing source and target node pairs.

Usage

addCyEdges(
  source.target.list,
  edgeType = "interacts with",
  directed = FALSE,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

A list of named lists of SUID, source and target for each edge added.

Examples

addCyEdges(c('sourceNode','targetNode'))
addCyEdges(list(c('s1','t1'),c('s2','t2')))

Description

Add one or more nodes to a Cytoscape network.

Usage

addCyNodes(
  node.names,
  skip.duplicate.names = TRUE,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

A list of named lists of name and SUID for each node added.

Examples

addCyNodes(c('Node A','Node B','Node C'))

Description

Adds the specified nodes and edges to the specified group.

Usage

AddToGroup(
  group.name,
  nodes = NULL,
  nodes.by.col = "SUID",
  edges = NULL,
  edges.by.col = "SUID",
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

None

Examples

AddToGroup('myGroup')

Description

Calculate various network statistics.

Usage

analyzeNetwork(directed = FALSE, base.url = .defaultBaseUrl)

Arguments

Details

The results are added to the Node and Edge tables and the Results Panel. The summary statistics in the Results Panel are also returned by the function as a list of named values.

Value

Named list of summary statistics

Examples

analyzeNetwork()
analyzeNetwork(TRUE)

Description

Run an existing filter by supplying the filter name.

Usage

applyFilter(
  filter.name = "Default filter",
  hide = FALSE,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Details

Known bug: selection (or hiding) of edges using edge-based column filters does not work. As a workaround, simply repeat the createColumnFilter operation to perform selection (or hiding) of edges.

Value

List of selected nodes and edges.

See Also

unhideAll

Examples

applyFilter('myFilter')
applyFilter('myFilter', hide = TRUE)

Description

Apply edge bundling to the network specified. Edge bundling is executed with default parameters; optional parameters are not supported.

Usage

bundleEdges(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

bundleEdges()

Description

checkNotebookIsRunning

Usage

checkNotebookIsRunning()

Value

None

Examples

checkNotebookIsRunning()

Description

Determine whether we're running locally or on a remote server. If locally (either via raw R or via a locally installed Notebook), we prefer to connect to Cytoscape over a local socket. If remote, we have to connect over Jupyter-Bridge. Either way, we can determine which by whether Cytoscape answers to a version check. If Cytoscape doesn't answer, we have no information ... and we have to wait until Cytoscape is started and becomes reachable before we can determine local vs remote.

Usage

checkRunningRemote(base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

checkRunningRemote()

Description

Clear all edge bends, e.g., those created from edge bundling.

Usage

clearEdgeBends(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

clearEdgeBends()

Description

Clear bypass values for any edge property of the specified edges, effectively restoring any previously defined style defaults or mappings.

Usage

clearEdgePropertyBypass(
  edge.names,
  visual.property,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

None

See Also

setEdgePropertyBypass

Examples

clearEdgePropertyBypass()

Description

Clear the bypass value for center x and y for the network, effectively restoring prior default values.

Usage

clearNetworkCenterBypass(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

clearNetworkCenterBypass()

Description

Clear bypass values for any network property, effectively restoring any previously defined style defaults or mappings.

Usage

clearNetworkPropertyBypass(
  visual.property,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

None

See Also

setNodePropertyBypass

Examples

clearNetworkPropertyBypass()

Description

Clear the bypass value for the scale factor for the network, effectively restoring prior default values.

Usage

clearNetworkZoomBypass(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

clearNetworkZoomBypass()

Description

Clear the bypass value for node fill, label and border opacity for the specified node or nodes, effectively restoring any previously defined style defaults or mappings.

Usage

clearNodeOpacityBypass(node.names, network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

See Also

setNodeOpacityBypass

Examples

clearNodeOpacityBypass(c('Node 1','Node 2'))

Description

Clear bypass values for any node property of the specified nodes, effectively restoring any previously defined style defaults or mappings.

Usage

clearNodePropertyBypass(
  node.names,
  visual.property,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

None

See Also

setNodePropertyBypass

Examples

clearNodePropertyBypass()

Description

If any nodes are selected in the network, they will be unselected.

Usage

clearSelection(type = "both", network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Author(s)

AlexanderPico, Tanja Muetze, Georgi Kolishovski, Paul Shannon

Examples

clearSelection()

Description

Makes a copy of a Cytoscape Network with all of its edges and nodes.

Usage

cloneNetwork(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

The suid of the new network

Author(s)

Alexander Pico, Julia Gustavsen

Examples

cloneNetwork("cloned network")

Description

Closes the current session in Cytoscape, destroying all unsaved work.

Usage

closeSession(save.before.closing, filename = NULL, base.url = .defaultBaseUrl)

Arguments

Details

A boolean for whether to save before closing is required since you could lose data by closing without saving.

Value

None

Examples

closeSession(FALSE)
closeSession(TRUE, '/fullpath/mySession')
closeSession(TRUE)

Description

Replaces the representation of all of the nodes and edges in a group with a single node.

Usage

collapseGroup(groups = NULL, network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

collapseGroup()

Description

The echo command will display the value of the variable specified by the variableName argument, or all variables if variableName is not provided.

Usage

commandEcho(variable.name = "*", base.url = .defaultBaseUrl)

Arguments

Value

Value of variable

Examples

commandEcho()

Description

The command line dialog provides a field to enter commands and view results. It also provides the help command to display namespaces, commands, and arguments

Usage

commandOpenDialog(base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

commandOpenDialog()

Description

The pause command displays a dialog with the text provided in the message argument and waits for the user to click OK.

Usage

commandPause(message = "", base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

commandPause('Please click OK to continue.')

Description

This command causes Cytoscape to exit. It is typically used at the end of a script file

Usage

commandQuit(base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

commandQuit()

Description

The run command will execute a command script from the file pointed to by the file argument, which should contain Cytoscape commands, one per line. Arguments to the script are provided by the args argument

Usage

commandRunFile(file, args = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

commandRunFile('/path/to/my/file.txt')

Description

Opens swagger docs in default browser for a live instance of Commands available via CyREST.

Usage

commandsAPI(base.url = .defaultBaseUrl)

Arguments

Value

Web page in browser

Examples

commandsAPI()

Description

Using the same syntax as Cytoscape's Command Line Dialog, this function converts a command string into a CyREST query URL, executes a GET request, and parses the result content into an R list object. The function check whether actual call is local or remote first. If remote, requests will go through Jupyter-Bridge. Extremely long commands may result in an immediate "URI Too Long" failure because 'commandsRun()' uses HTTP GET to call the CyREST API, and HTTP GET has known limitations. You can use 'commandsPost()' instead, though the return value will be different. 'commandsPost()' uses HTTP POST, which has no limitations.

Usage

commandsGET(cmd.string, base.url = .defaultBaseUrl)

Arguments

Value

A list, status or None.

Examples

commandsGET('layout get preferred network=current')
commandsGET('network list properties network=current')
commandsGET('layout force-directed defaultNodeMass=1')

Description

Using the same syntax as Cytoscape's Command Line Dialog, this function returns a list of available commands or args. The function check whether actual call is local or remote first. If remote, requests will go through Jupyter-Bridge.

Usage

commandsHelp(cmd.string = "help", base.url = .defaultBaseUrl)

Arguments

Details

Works with or without 'help' command prefix. Note that if you ask about a command that doesn't have any arguments, this function will run the command!

Value

List of available commands or args

Examples

commandsHelp()
commandsHelp('node')
commandsHelp('node get attribute')

Description

The sleep command will pause processing for a period of time as specified by duration seconds. It is typically used as part of a command script.

Usage

commandSleep(duration = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

commandSleep(5)

Description

Using the same syntax as Cytoscape's Command Line Dialog, this function converts a command string into a CyREST query URL, executes a POST request, and parses the result content into an R list object. The function check whether actual call is local or remote first. If remote, requests will go through Jupyter-Bridge.

Usage

commandsPOST(cmd.string, base.url = .defaultBaseUrl)

Arguments

Value

A list, named list, status or None.

Examples

commandsPOST('layout get preferred')
commandsPOST('network list properties')
commandsPOST('layout force-directed defaultNodeMass=1')

Description

Using the same syntax as Cytoscape's Command Line Dialog, this function converts a command string into a CyREST query URL, executes a GET request, and parses the result content into an R list object. Same as commandsGET. Extremely long commands may result in an immediate "URI Too Long" failure because 'commandsRun()' uses HTTP GET to call the CyREST API, and HTTP GET has known limitations. You can use 'commandsPost()' instead, though the return value will be different. 'commandsPost()' uses HTTP POST, which has no limitations.

Usage

commandsRun(cmd.string, base.url = .defaultBaseUrl)

Arguments

Value

A list, status or None.

Examples

commandsRun('layout get preferred')
commandsRun('network list properties')
commandsRun('layout force-directed defaultNodeMass=1')

Description

Create a new visual style by copying a specified style.

Usage

copyVisualStyle(from.style, to.style, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

copyVisualStyle()

Description

Creates a filter to control node or edge selection. Works on columns of boolean, string, numeric and lists. Note the unique restrictions for criterion and predicate depending on the type of column being filtered.

Usage

createColumnFilter(
  filter.name,
  column,
  criterion,
  predicate,
  caseSensitive = FALSE,
  anyMatch = TRUE,
  type = "nodes",
  hide = FALSE,
  network = NULL,
  base.url = .defaultBaseUrl,
  apply = TRUE
)

Arguments

Value

List of selected nodes and edges.

Examples

createColumnFilter('myFilter', 'log2FC', c(-1,1), "IS_NOT_BETWEEN")
createColumnFilter('myFilter', 'pValue', 0.05, "LESS_THAN")
createColumnFilter('myFilter', 'function', "kinase", "CONTAINS", FALSE)
createColumnFilter('myFilter', 'name', "^Y.*C$", "REGEX")
createColumnFilter('myFilter', 'isTarget', TRUE , "IS", apply=FALSE)
createColumnFilter('myFilter', 'isTarget', TRUE , "IS", hide=TRUE)

Description

Combines filters to control node and edge selection based on previously created filters.

Usage

createCompositeFilter(
  filter.name,
  filter.list,
  type = "ALL",
  hide = FALSE,
  network = NULL,
  base.url = .defaultBaseUrl,
  apply = TRUE
)

Arguments

Value

List of selected nodes and edges.

Examples

createCompositeFilter("comp1", c("filter1", "filter2"))
createCompositeFilter("comp2", c("filter1", "filter2"), "ANY")
createCompositeFilter("comp3", c("comp1", "filter3"), apply=FALSE)

Description

Create a Cytoscape JS representation of a Cytoscape network

Usage

createCytoscapejsFromNetwork(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

(list) The Cytoscape JS object

Examples

createCytoscapejsFromNetwork()

Description

Creates a filter to control node selection base on in/out degree.

Usage

createDegreeFilter(
  filter.name,
  criterion,
  predicate = "BETWEEN",
  edgeType = "ANY",
  hide = FALSE,
  network = NULL,
  base.url = .defaultBaseUrl,
  apply = TRUE
)

Arguments

Value

List of selected nodes and edges.

Examples

createDegreeFilter('myFilter', c(4,5))
createDegreeFilter('myFilter', c(2,5), apply=FALSE)

Description

Returns the Cytoscape network as a Bioconductor graph.

Usage

createGraphFromNetwork(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

A Bioconductor graph object.

Author(s)

Alexander Pico, Tanja Muetze, Georgi Kolishovski, Paul Shannon

Examples

cw <- CytoscapeWindow('network', graph=make_graphnel())
g <- createGraphFromNetwork()
g <- createGraphFromNetwork('myNetwork')

Description

Create a group from the specified nodes.

Usage

createGroup(
  group.name,
  nodes = NULL,
  nodes.by.col = "SUID",
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

Group SUID

Examples

createGroup('myGroup')

Description

Create a group of nodes defined by a column value.

Usage

createGroupByColumn(
  group.name,
  column = NULL,
  value = NULL,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

Group SUID

Examples

createGroupByColumn('myGroup','Cluster', 'A')

Description

Takes a Cytoscape network and generates data frames for vertices and edges to send to the graph_from_data_frame function. Returns the network.suid and applies the perferred layout set in Cytoscape preferences.

Usage

createIgraphFromNetwork(network = NULL, base.url = .defaultBaseUrl)

Arguments

Details

Nodes and edges from the Cytoscape network will be translated into vertices and edges in igraph. Associated table columns will also be passed to igraph as vertiex and edge attributes. Note: all networks are implicitly modeled as directed in Cytoscape. Round-trip conversion of an undirected network in igraph via createNetworkFromIgraph to Cytoscape and back to igraph will result in a directed network.

Value

(igraph) an igraph network

See Also

createNetworkFromDataFrames, createNetworkFromIgraph

Examples

ig <- createIgraphFromNetwork()
ig <- createIgraphFromNetwork('myNetwork')

Description

Create a network from CytoscapeJS JSON

Usage

createNetworkFromCytoscapejs(
  cytoscapejs,
  title = NULL,
  collection = "My CytoscapeJS Network Collection",
  base.url = .defaultBaseUrl
)

Arguments

Value

The SUID of the new network

Examples

createNetworkFromCytoscapejs()

Description

Takes data frames for nodes and edges, as well as naming parameters to generate the JSON data format required by the "networks" POST operation via CyREST. Returns the network.suid and applies the perferred layout set in Cytoscape preferences.

Usage

createNetworkFromDataFrames(
  nodes = NULL,
  edges = NULL,
  title = "From dataframe",
  collection = "My Dataframe Network Collection",
  base.url = .defaultBaseUrl,
  ...
)

Arguments

Details

NODES should contain a column of character strings named: id. This name can be overridden by the arg: node.id.list. Additional columns are loaded as node attributes. EDGES should contain columns of character strings named: source, target and interaction. These names can be overridden by args: source.id.list, target.id.list, interaction.type.list. Additional columns are loaded as edge attributes. The 'interaction' list can contain a single value to apply to all rows; and if excluded altogether, the interaction type wiil be set to "interacts with". NOTE: attribute values of types (num) will be imported as (Double); (int) as (Integer); (chr) as (String); and (logical) as (Boolean). (Lists) will be imported as (Lists) in CyREST v3.9+.

Value

(int) network SUID

Examples

nodes <- data.frame(id=c("node 0","node 1","node 2","node 3"),
           group=c("A","A","B","B"), # categorical strings
           score=as.integer(c(20,10,15,5))) # integers
edges <- data.frame(source=c("node 0","node 0","node 0","node 2"),
           target=c("node 1","node 2","node 3","node 3"),
           interaction=c("inhibits","interacts",
                         "activates","interacts"),  # optional
           weight=c(5.1,3.0,5.2,9.9)) # numeric

createNetworkFromDataFrames(nodes,edges)

Description

Creates a Cytoscape network from a Bioconductor graph.

Usage

createNetworkFromGraph(
  graph,
  title = "From graph",
  collection = "My GraphNEL Network Collection",
  base.url = .defaultBaseUrl
)

Arguments

Value

Network SUID

Author(s)

Alexander Pico, Tanja Muetze, Georgi Kolishovski, Paul Shannon

Examples

library(graph)
g <- makeSimpleGraph()
createNetworkFromGraph(g)

Description

Takes an igraph network and generates data frames for nodes and edges to send to the createNetwork function. Returns the network.suid and applies the perferred layout set in Cytoscape preferences.

Usage

createNetworkFromIgraph(
  igraph,
  title = "From igraph",
  collection = "My Igraph Network Collection",
  base.url = .defaultBaseUrl,
  ...
)

Arguments

Details

Vertices and edges from the igraph network will be translated into nodes and edges in Cytoscape. Associated attributes will also be passed to Cytoscape as node and edge table columns. Note: undirected networks will be implicitly modeled as directed in Cytoscape. Conversion back via createIgraphFromNetwork will result in a directed network. Also note: igraph attributes of type "other" denoted by "x" are converted to "String" in Cytoscape.

Value

(int) network SUID

See Also

createNetworkFromDataFrames, createIgraphFromNetwork

Examples

library(igraph)
ig <- makeSimpleIgraph()
createNetworkFromIgraph(ig)

Description

Copies a subset of nodes and edges into a newly created subnetwork.

Usage

createSubnetwork(
  nodes = NULL,
  nodes.by.col = "SUID",
  edges = NULL,
  edges.by.col = "SUID",
  exclude.edges = FALSE,
  subnetwork.name = NULL,
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Details

If you specify both nodes and edges, the resulting subset will be the union of those sets. Typical usage only requires specifying either nodes or edges. Note that selected nodes will bring along their connecting edges by default (see exclude.edges arg) and selected edges will always bring along their source and target nodes.

Value

SUID of new subnetwork

Examples

createSubnetwork()
createSubnetwork("all")
createSubnetwork(subnetwork.name="mySubnetwork")
createSubnetwork(c("node 1","node 2","node 3"),"name")
createSubnetwork(c("AKT1","TP53","PIK3CA"),"display name")
createSubnetwork(edges="all") #subnetwork of all connected nodes

Description

Create a network view if one does not already exist

Usage

createView(layout = TRUE, network = NULL, base.url = .defaultBaseUrl)

Arguments

Details

For networks larger than the view creation threshold, a network view is not created by default. This function creates a network view if one does not already exist.

Value

Network view SUID

Examples

getNetworkViews()

Description

Create a style from defaults and predefined mappings.

Usage

createVisualStyle(style.name, defaults, mappings, base.url = .defaultBaseUrl)

Arguments

Details

Requires attribute mappings to be previously created, see mapVisualProperty.

Value

None

See Also

applyStyle, mapVisualProperty

Examples

#first there has to be a network to apply style to
example(createNetworkFromDataFrames)

#then prepare style variables
style.name = "myStyle"
defaults <- list(NODE_SHAPE="diamond",
                 NODE_SIZE=30,
                 EDGE_TRANSPARENCY=120,
                 NODE_LABEL_POSITION="W,E,c,0.00,0.00")
nodeLabels <- mapVisualProperty('node label','id','p')
nodeFills <- mapVisualProperty('node fill color','group','d',c("A","B"), c("#FF9900","#66AAAA"))
arrowShapes <- mapVisualProperty('Edge Target Arrow Shape','interaction','d',
                                 c("activates","inhibits","interacts"),c("Arrow","T","None"))
edgeWidth <- mapVisualProperty('edge width','weight','p')

#and then create the style
createVisualStyle(style.name, defaults, list(nodeLabels,nodeFills,arrowShapes,edgeWidth))

#finsh by applying the style
setVisualStyle(style.name)

Description

Close an internal web browser and remove all content. Provide an id for the browser you want to close.

Usage

cybrowserClose(id = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

cybrowserClose('554')

Description

Launch Cytoscape's internal web browser in a separate window. Provide an id for the window if you want subsequent control of the window e.g., via cybrowser hide.

Usage

cybrowserDialog(
  id = NULL,
  text = NULL,
  title = NULL,
  url = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

None

See Also

cybrowserShow

cybrowserHide

Examples

cybrowserDialog(url='http://cytoscape.org')

Description

Hide an existing browser, whether it's in the Results panel or a separate window.

Usage

cybrowserHide(id = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

See Also

cybrowserShow

cybrowserDialog

Examples

cybrowserHide()

Description

List all browsers that are currently open, whether as a dialog or in the results panel.

Usage

cybrowserList(base.url = .defaultBaseUrl)

Arguments

Value

List of open cybrowser windows

Examples

cybrowserList()

Description

Send the text to the browser indicated by the id and return the response, if any. Note that the JSON result field could either be a bare string or JSON formatted text.

Usage

cybrowserSend(id = NULL, script, base.url = .defaultBaseUrl)

Arguments

Value

String result

Examples

cybrowserSend(id="Window 1", script="navigator.userAgent;")

Description

Launch Cytoscape's internal web browser in a pane in the Result Panel. Provide an id for the window if you want subsequent control of the window via cybrowser hide.

Usage

cybrowserShow(
  id = NULL,
  text = NULL,
  title = NULL,
  url = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

None

See Also

cybrowserDialog

cybrowserHide

Examples

cybrowserShow(url='http://cytoscape.org')

Description

Display the version of the CyBrowser app.

Usage

cybrowserVersion(base.url = .defaultBaseUrl)

Arguments

Value

Version number

Examples

cybrowserVersion()

Description

Opens swagger docs in default browser for a live instance of CyREST operations.

Usage

cyrestAPI(base.url = .defaultBaseUrl)

Arguments

Value

Web page in browser

Examples

cyrestAPI()

Description

Constructs the query, makes DELETE call and processes the result. The function check whether actual call is local or remote first. If remote, requests will go through Jupyter-Bridge.

Usage

cyrestDELETE(operation = NULL, parameters = NULL, base.url = .defaultBaseUrl)

Arguments

Value

CyREST result content

Examples

cyrestDELETE('session')

Description

Constructs the query, makes GET call and processes the result. The function check whether actual call is local or remote first. If remote, requests will go through Jupyter-Bridge.

Usage

cyrestGET(operation = NULL, parameters = NULL, base.url = .defaultBaseUrl)

Arguments

Value

CyREST result content

Examples

cyrestGET('version')

Description

Constructs the query and body, makes POST call and processes the result. The function check whether actual call is local or remote first. If remote, requests will go through Jupyter-Bridge.

Usage

cyrestPOST(
  operation,
  parameters = NULL,
  body = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

CyREST result content

Examples

cyrestPOST('networks/51/views')

Description

Constructs the query and body, makes PUT call and processes the result. The function check whether actual call is local or remote first. If remote, requests will go through Jupyter-Bridge.

Usage

cyrestPUT(
  operation,
  parameters = NULL,
  body = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

CyREST result content

Examples

cyrestPUT()

Description

Get the list of available CyREST API versions

Usage

cytoscapeApiVersions(base.url = .defaultBaseUrl)

Arguments

Value

A list of API versions as character strings, e.g., "v1"

Author(s)

Alexander Pico, Tanja Muetze, Georgi Kolishovski, Paul Shannon

Examples

cytoscapeApiVersions()
# [1] "v1"

Description

Manually call Java's garbage collection System.gc() to free up unused memory. This process happens automatically, but may be useful to call explicitly for testing or evaluation purposes.

Usage

cytoscapeFreeMemory(base.url = .defaultBaseUrl)

Arguments

Value

status message

Author(s)

Alexander Pico

Examples

cytoscapeFreeMemory()
# [1] "Unused memory freed up."

Description

Returns the memory resources of the server running Cytoscape

Usage

cytoscapeMemoryStatus(base.url = .defaultBaseUrl)

Arguments

Value

A list of numeric values

Author(s)

Alexander Pico

Examples

cytoscapeMemoryStatus()
#  usedMemory  freeMemory totalMemory   maxMemory 
#         181        2624        2805       13653

Description

Returns the processor resources of the server running Cytoscape

Usage

cytoscapeNumberOfCores(base.url = .defaultBaseUrl)

Arguments

Value

A numeric value

Author(s)

Alexander Pico

Examples

cytoscapeNumberOfCores()
# [1] 8

Description

Tests the connection to Cytoscape via CyREST and verifies that supported versions of Cytoscape and CyREST API are loaded.

Usage

cytoscapePing(base.url = .defaultBaseUrl)

Arguments

Value

status message

Author(s)

Alexander Pico, Tanja Muetze, Georgi Kolishovski, Paul Shannon

Examples

cytoscapePing()
# [1] "You are connected to Cytoscape!"

Description

Returns the versions of the current Cytoscape and CyREST API

Usage

cytoscapeVersionInfo(base.url = .defaultBaseUrl)

Arguments

Value

list of versions

Author(s)

Alexander Pico

Examples

cytoscapeVersionInfo()
 # apiVersion cytoscapeVersion 
 #       "v1" "3.7.0-SNAPSHOT"

Description

Delete all networks from the current Cytoscape session.

Usage

deleteAllNetworks(base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

deleteAllNetworks()

Description

Delete all visual styles from current Cytoscape session

Usage

deleteAllVisualStyle(base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

deleteAllVisualStyle()

Description

Remove an annotation from the current network view in Cytoscape

Usage

deleteAnnotation(names = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

deleteAnnotation("016a4af1-69bc-4b99-8183-d6f118847f96")
deleteAnnotation(c("T2","T3"))
deleteAnnotation(sapply(getAnnotationList(), '[[', 'uuid'))

Description

Removes edges with duplicate names. Only considers cases with identical source, target, interaction and directionality.

Usage

deleteDuplicateEdges(network = NULL, base.url = .defaultBaseUrl)

Arguments

Details

Duplicate edges are first selected and then deleted. Prior edge selections will be lost; node selections will not be affected.

Value

Lists of SUIDs for selected nodes and edges

Examples

deleteDuplicateEdges()

Description

Deletes one or more groups, while leaving member nodes intact.

Usage

deleteGroup(
  groups = NULL,
  groups.by.col = "SUID",
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Details

Note: group nodes are ungrouped but not deleted in Cytoscape version 3.6.1

Value

None

Examples

deleteGroup()

Description

Delete a network from the current Cytoscape session.

Usage

deleteNetwork(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

deleteNetwork()

Description

Delete the currently selected edges in the network.

Usage

deleteSelectedEdges(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

list of deleted edge SUIDs

Author(s)

AlexanderPico, Tanja Muetze, Georgi Kolishovski, Paul Shannon

Examples

deleteSelectedEdges()

Description

Delete currently selected nodes from the network.

Usage

deleteSelectedNodes(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

A named list of deleted node suids ($nodes) as well as edge suids ($edges) deleted as a result of the node deletion

Examples

deleteSelectedNodes()

Description

Removes edges that connect to a single node as both source and target.

Usage

deleteSelfLoops(network = NULL, base.url = .defaultBaseUrl)

Arguments

Details

Self loop edges are first selected and then deleted. Prior edge and node selections will be lost.

Value

Lists of SUIDs for selected nodes and edges

Examples

deleteSelfLoops()

Description

Deletes a specified visual style mapping from specified style.

Usage

deleteStyleMapping(style.name, visual.prop, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

deleteStyleMapping()

Description

Delete a column from node, edge or network tables.

Usage

deleteTableColumn(
  column,
  table = "node",
  namespace = "default",
  network = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Value

A data.frame of column values

Examples

deleteTableColumn('node','group')

Description

Deletes the specified visual style from current session.

Usage

deleteVisualStyle(style.name, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

deleteVisualStyle("myStyle")

Description

Diffusion will send the selected network view and its selected nodes to a web-based REST service to calculate network propagation. Results are returned and represented by columns in the node table. Advanced operation supports parameters.

Usage

diffusionAdvanced(
  heat.column.name = NULL,
  time = NULL,
  base.url = .defaultBaseUrl
)

Arguments

Details

Columns are created for each execution of Diffusion and their names are returned in the response. The nodes you would like to use as input should be selected. This will be used to generate the contents of the diffusion_input column, which represents the query vector and corresponds to h in the diffusion equation.

Value

Version number

Examples

diffusionAdvanced()

Description

Diffusion will send the selected network view and its selected nodes to a web-based REST service to calculate network propagation. Results are returned and represented by columns in the node table.

Usage

diffusionBasic(base.url = .defaultBaseUrl)

Arguments

Details

Columns are created for each execution of Diffusion and their names are returned in the response. The nodes you would like to use as input should be selected. This will be used to generate the contents of the diffusion_input column, which represents the query vector and corresponds to h in the diffusion equation.

Value

Version number

Examples

diffusionBasic()

Description

Disable an app to effectively remove it from your Cytoscape session without having to uninstall it.

Usage

disableApp(app, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

disableApp()

Description

Dock a panel back into the UI of Cytoscape.

Usage

dockPanel(panel.name, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

dockPanel('table')

Description

doInitializeSandbox

Usage

doInitializeSandbox(requester = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

doInitializeSandbox()

Description

Do requests remotely by connecting over Jupyter-Bridge.

Usage

doRequestRemote(method, qurl, qbody = NULL, headers = NULL)

Arguments

Value

httr response

Examples

doRequestRemote()

Description

doSetSandbox

Usage

doSetSandbox(sandboxToSet, requester = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

doSetSandbox()

Description

Enable a previously installed and disabled app in Cytoscape.

Usage

enableApp(app, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

enableApp()

Description

Replaces the group node with member nodes for a set of groups.

Usage

expandGroup(groups = NULL, network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

expandGroup()

Description

Saves filters to file in JSON format.

Usage

exportFilters(
  filename = "filters.json",
  base.url = .defaultBaseUrl,
  overwriteFile = TRUE
)

Arguments

Details

Unlike other export functions, Cytoscape will automatically overwrite files with the same name. You will not be prompted to confirm or reject overwrite. Use carefully!

Value

None

Examples

exportFilters()

Description

Saves the current network view as an image file.

Usage

exportImage(
  filename = NULL,
  type = "PNG",
  resolution = NULL,
  units = NULL,
  height = NULL,
  width = NULL,
  zoom = NULL,
  network = NULL,
  base.url = .defaultBaseUrl,
  overwriteFile = TRUE
)

Arguments

Details

The image is cropped per the current view in Cytoscape. Consider applying fitContent prior to export.

Value

server response

Examples

exportImage('/fullpath/myNetwork','PDF')

Description

Saves the current network view as an jpg file.

Usage

exportJPG(
  filename = NULL,
  allGraphicsDetails = TRUE,
  hideLabels = FALSE,
  zoom = NULL,
  network = NULL,
  base.url = .defaultBaseUrl,
  overwriteFile = TRUE
)

Arguments

Details

Exports the current view to a graphics file and returns the path to the saved file. To speed up image export for large networks use the option 'allGraphicsDetails=FALSE'. Available for Cytoscape v3.10 or later.

Value

server response

Examples

exportJPG('/fullpath/myNetwork')

Description

Export a network to one of mulitple file formats

Usage

exportNetwork(
  filename = NULL,
  type = "SIF",
  network = NULL,
  base.url = .defaultBaseUrl,
  overwriteFile = TRUE
)

Arguments

Value

None.

Examples

exportNetwork('/path/filename','SIF')

Description

Send a copy of a Cytoscape network to NDEx as a new submission.

Usage

exportNetworkToNDEx(
  username,
  password,
  isPublic,
  network = NULL,
  metadata = NULL,
  ndex.url = "http://ndexbio.org",
  ndex.version = "v2",
  base.url = .defaultBaseUrl
)

Arguments

Value

NDEx identifier (externalId) for new submission

Examples

exportNetworkToNDEx("user", "pass", TRUE)

Description

Saves the current network view as an pdf file.

Usage

exportPDF(
  filename = NULL,
  exportTextAsFont = TRUE,
  hideLabels = FALSE,
  pageSize = "Letter",
  orientation = "Portrait",
  network = NULL,
  base.url = .defaultBaseUrl,
  overwriteFile = TRUE
)

Arguments

Details

Exports the current view to a graphics file and returns the path to the saved file. To speed up image export for large networks use the option 'allGraphicsDetails=FALSE'. Available for Cytoscape v3.10 or later.

Value

server response

Examples

exportPDF('/fullpath/myNetwork')

Description

Saves the current network view as an png file.

Usage

exportPNG(
  filename = NULL,
  allGraphicsDetails = TRUE,
  hideLabels = FALSE,
  transparentBackground = FALSE,
  zoom = NULL,
  network = NULL,
  base.url = .defaultBaseUrl,
  overwriteFile = TRUE
)

Arguments

Details

Exports the current view to a graphics file and returns the path to the saved file. To speed up image export for large networks use the option 'allGraphicsDetails=FALSE'. Available for Cytoscape v3.10 or later.

Value

server response

Examples

exportPNG('/fullpath/myNetwork')

Description

Saves the current network view as an ps file.

Usage

exportPS(
  filename = NULL,
  exportTextAsFont = TRUE,
  hideLabels = FALSE,
  network = NULL,
  base.url = .defaultBaseUrl,
  overwriteFile = TRUE
)

Arguments

Details

Exports the current view to a graphics file and returns the path to the saved file. To speed up image export for large networks use the option 'allGraphicsDetails=FALSE'. Available for Cytoscape v3.10 or later.

Value

server response

Examples

exportPS('/fullpath/myNetwork')

Description

Saves the current network view as an svg file.

Usage

exportSVG(
  filename = NULL,
  exportTextAsFont = TRUE,
  hideLabels = FALSE,
  network = NULL,
  base.url = .defaultBaseUrl,
  overwriteFile = TRUE
)

Arguments

Details

Exports the current view to a graphics file and returns the path to the saved file. To speed up image export for large networks use the option 'allGraphicsDetails=FALSE'. Available for Cytoscape v3.10 or later.

Value

server response

Examples

exportSVG('/fullpath/myNetwork')

Description

Save one or more visual styles to file.

Usage

exportVisualStyles(
  filename = NULL,
  type = "XML",
  styles = NULL,
  base.url = .defaultBaseUrl,
  overwriteFile = TRUE
)

Arguments

Value

Path to saved file

See Also

importVisualStyles

Examples

exportVisualStyles('/fullpath/myStyle')
exportVisualStyles('/fullpath/myStyle', type = 'JSON')
exportVisualStyles('/fullpath/myStyle', style = 'Minimal,default,Directed')

Description

Figure out whether CyREST is local or remote. If remote, we'll want to go through Jupyter-Bridge.

Usage

findRemoteCytoscape(base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

findRemoteCytoscape()

Description

Zoom and pan network view to maximize either height or width of current network window.

Usage

fitContent(selected.only = FALSE, network = NULL, base.url = .defaultBaseUrl)

Arguments

Details

Takes first (presumably only) view associated with provided network

Value

None

Examples

fitContent()

Description

Pop out a panel from the UI of Cytoscape. Other panels will expand into the space.

Usage

floatPanel(panel.name, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

floatPanel('table')

Description

Get absolute sandbox path.

Usage

getAbsSandboxPath(fileLocation)

Arguments

Value

file location

Examples

getAbsSandboxPath()

Description

Retrieve the names of all the edges in the network.

Usage

getAllEdges(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

list of node edges

Examples

getAllEdges()

Description

Retrieve the names of all the nodes in the network.

Usage

getAllNodes(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

list of node names

Examples

getAllNodes()

Description

Retrieve the values the define all the mappings per visual property in a given style.

Usage

getAllStyleMappings(style.name = NULL, base.url = .defaultBaseUrl)

Arguments

Value

List of lists with named values defining the visual property mappings

Examples

getStyleMapping()

Description

A list of named lists with annotation information

Usage

getAnnotationList(network = NULL, base.url = .defaultBaseUrl)

Arguments

Details

You can obtain a list of UUIDs by applying a subset function like so: sapply(getAnnotationList(), '[[', 'uuid')

Value

RETURN_DESCRIPTION

Examples

getAnnotationList()

Description

Retrieve the name, brief description and version of a Cytoscape app.

Usage

getAppInformation(app, base.url = .defaultBaseUrl)

Arguments

Value

App name, brief description and version.

Examples

getAppInformation()

Description

Retrieve the current status of a Cytoscape app: Installed, Uninstalled or Disabled.

Usage

getAppStatus(app, base.url = .defaultBaseUrl)

Arguments

Value

App name and status

Examples

getAppStatus()

Description

Retrieve list of currently installed Cytoscape apps with updates available.

Usage

getAppUpdates(base.url = .defaultBaseUrl)

Arguments

Value

A list of updatable app names, versions and statuses

Examples

getAppUpdates()

Description

Retrieve the names of the currently supported 'arrows' – the decorations can (optionally) appear at the ends of edges, adjacent to the nodes they connect, and conveying information about the nature of the nodes' relationship.

Usage

getArrowShapes(base.url = .defaultBaseUrl)

Arguments

Value

A list of character strings, e.g., 'DIAMOND', 'T', 'ARROW'

Examples

getArrowShapes()

Description

Retrieve a list of apps available for installation in Cytoscape.

Usage

getAvailableApps(base.url = .defaultBaseUrl)

Arguments

Value

A list of app names and latest versions

Examples

getAvailableApps()

Description

Retrieve the default background color.

Usage

getBackgroundColorDefault(style.name = NULL, base.url = .defaultBaseUrl)

Arguments

Value

None

Examples

getBackgroundColorDefault()

Description

Get the unique channel

Usage

getBrowserClientChannel()

Value

client channel

Examples

getBrowserClientChannel()

Description

Prepend channel number of client Javascript so it can communicate with this process via Jupyter-bridge

Usage

getBrowserClientJs()

Value

Javascript inject code

Examples

getBrowserClientJs()

Description

FUNCTION_DESCRIPTION

Usage

getCollectionList(base.url = .defaultBaseUrl)

Arguments

Value

RETURN_DESCRIPTION

Examples

getCollectionList()

Description

FUNCTION_DESCRIPTION

Usage

getCollectionName(collection.suid = NULL, base.url = .defaultBaseUrl)

Arguments

Value

RETURN_DESCRIPTION

Examples

getCollectionName()

Description

FUNCTION_DESCRIPTION

Usage

getCollectionNetworks(collection.suid = NULL, base.url = .defaultBaseUrl)

Arguments

Value

RETURN_DESCRIPTION

Examples

getCollectionNetworks()

Description

FUNCTION_DESCRIPTION

Usage

getCollectionSuid(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

RETURN_DESCRIPTION

Examples

getCollectionSuid()

Description

Return both the current sandbox name and path.

Usage

getCurrentSandbox()

Value

current sandbox

Examples

getCurrentSandbox()

Description

Return the current sandbox name.

Usage

getCurrentSandboxName()

Value

current sandbox name

Examples

getCurrentSandboxName()

Description

Return the current sandbox path.

Usage

getCurrentSandboxPath()

Value

current sandbox path

Examples

getCurrentSandboxPath()

Description

Get the current visual style applied to a network.

Usage

getCurrentStyle(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

Name of style

Examples

getCurrentStyle()
getCurrentStyle('myNetwork')

Description

Return whatever is the current default sandbox properties.

Usage

getDefaultSandbox()

Value

default sandbox

Examples

getDefaultSandbox()

Description

Return the default path, which isn't one of the properties tracked in the default_sandbox.

Usage

getDefaultSandboxPath()

Value

default sandbox path

Examples

getDefaultSandboxPath()

Description

Retrieve list of currently disabled apps in Cytoscape.

Usage

getDisabledApps(base.url = .defaultBaseUrl)

Arguments

Value

A list of disabled app names, versions and statuses

Examples

getDisabledApps()

Description

Retrieve the actual line color of specified edges.

Usage

getEdgeColor(edge.names = NULL, network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

Named list of property values

Examples

getEdgeColor()

Description

Reports the number of the edges in the network.

Usage

getEdgeCount(network = NULL, base.url = .defaultBaseUrl)

Arguments

Value

numeric

Author(s)

Alexander Pico, Tanja Muetze, Georgi Kolishovski, Paul Shannon

Examples

getEdgeCount()

Description

Returns source, target and edge table row values.

Usage

getEdgeInfo(edges, network = NULL, base.url = .defaultBaseUrl)

Arguments

Details

This function is kinda slow. It takes approximately 70ms per edge to return a result, e.g., 850 edges will take a one minute.

Value

named list of lists