Package 'RCyjs'

Title: Display and manipulate graphs in cytoscape.js
Description: Interactive viewing and exploration of graphs, connecting R to Cytoscape.js, using websockets.
Authors: Paul Shannon
Maintainer: Paul Shannon <[email protected]>
License: MIT + file LICENSE
Version: 2.29.0
Built: 2024-11-18 04:08:33 UTC
Source: https://github.com/bioc/RCyjs

Help Index

addGraph

Description

addGraph send these nodes and edges (with attributes) to RCyjs for display

Usage

## S4 method for signature 'RCyjs'
addGraph(obj, graph)

Arguments

obj

an RCyjs instance
graph

a graphNEL

Details

This version transmits a graph (nodes, edges and attributes) to the browser by writing the data to a file, and sending that filename to be read in the browser by javascript.

Value

nothing

Examples

if(interactive()){
  rcy <- RCyjs(title="rcyjs demo", graph=g)
  g <- simpleDemoGraph()
  setGraph(rcy, g)
  }

addGraphFromFile

Description

addGraphFromFile add graph from specified file, which contains a cytoscape.js JSON graph

Usage

## S4 method for signature 'RCyjs'
addGraphFromFile(obj, jsonFileName)

Arguments

obj

an RCyjs instance
jsonFileName

path to the file

Details

More description

Value

nothin

Examples

if(interactive()){
  rcy <- RCyjs()
  filename <- system.file(package="RCyjs", "extdata", "sampleGraph.json")
  addGraphFromFile(rcy, filename)
  layout(rcy, "cose")
  fit(rcy, 200)
  }

clearSelection

Description

clearSelection deselect all selected nodes, all selected edges, or both

Usage

## S4 method for signature 'RCyjs'
clearSelection(obj, which = "both")

Arguments

obj

an RCyjs object
which

a character string: "both" (the default), "nodes" or "edges"

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   selectNodes(rcy, c("A", "B"))
   clearSelection(rcy)
   }

createTestGraph

Description

createTestGraph With as many nodes and edges as you wish, but neither edge nor node attributes.

Usage

createTestGraph(nodeCount, edgeCount)

Arguments

nodeCount

1 or more
edgeCount

0 or more

Value

a graphNEL with nodeCount nodes and edgeCount edges

Examples

g <- createTestGraph(5, 3)

Create a cytoscape.js JSON graph from one or two data.frames.

Description

Create a cytoscape.js JSON graph from one or two data.frames.

Usage

dataFramesToJSON(tbl.edges, tbl.nodes = NULL)

Arguments

tbl.edges

data.frame, with source, target and interaction columns, others option for edge attributes
tbl.nodes

data.frame, options, useful for orphan nodes, and necessary for adding node attributes

deleteGraph

Description

deleteGraph Remove all nodes and edges, the elements of the current graph.

Usage

## S4 method for signature 'RCyjs'
deleteGraph(obj)

Arguments

obj

RCyjs instance

Details

This method will remove any previous graph in the browser

Value

nothing

See Also

addGraph setGraph

Examples

if(interactive()){
  sampleGraph <- simpleDemoGraph()
  rcy <- RCyjs(title="rcyjs demo", graph=sampleGraph)
  deletetGraph(rcy)
  }

deleteSelectedNodes

Description

deleteSelectedNodes put somewhat more detailed description here

Usage

## S4 method for signature 'RCyjs'
deleteSelectedNodes(obj)

Arguments

obj

an RCyjs instance

Details

multi-line description goes here with continuations on subsequent lines if you like

Value

explain what the method returns

Examples

if(interactive()){
   g <- simpleDemoGraph()
   rcy <- RCyjs(title="rcyjs demo", graph=g)
   target <- nodes(g)[1]
   selectNodes(rcy, target)
   deleteSelectedNodes(rcy)
   }

eda

Description

eda retrieve the node/attribute-value pairs, for the specified node attribute category

Usage

eda(graph, edge.attribute.name)

Arguments

graph

a graphNEL
edge.attribute.name

a character string

Value

character strings, the names of the unique edge attribute categories on the graph

Examples

if(interactive()){
  g <- simpleDemoGraph()
  edaNames(g)   # discover the attribute category names
  eda(g, "edgeType")
  eda(g, "score")
  }

edaNames

Description

edaNames the names of the unique edge attribute categories on the graph (not their values)

Usage

edaNames(graph)

Arguments

graph

a graphNEL

Value

character strings, the names of the unique edge attribute categories on the graph

Examples

if(interactive()){
  g <- simpleDemoGraph()
  edaNames(g)
  }

fit

Description

fit zoom in (or out) to display all nodes in the current graph

Usage

## S4 method for signature 'RCyjs'
fit(obj, padding = 30)

Arguments

obj

an RCyjs instance
padding

numeric, in pixels

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   setZoom(rcy, 0.5)   # zoom out
   fit(rcy)
   }

fitSelection

Description

fitSelection zoom in to include only currently selected nodes

Usage

## S4 method for signature 'RCyjs'
fitSelection(obj, padding = 30)

Arguments

obj

an RCyjs instance
padding

numeric, in pixels

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   selectNodes(rcy, "A")
   fitSelection(rcy, padding=100)
   }

getEdgeCount

Description

getEdgeCount the number of edges in the current cytoscape.js graph

Usage

## S4 method for signature 'RCyjs'
getEdgeCount(obj)

Arguments

obj

RCyjs instance

Value

numeric count

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   getEdgeCount(rcy)
   }

getJSON

Description

getJSON a JSON string from the browser, describing the graph in cytoscape.js terms

Usage

## S4 method for signature 'RCyjs'
getJSON(obj)

Arguments

obj

an RCyjs instance

Value

a JSON string

Examples

if(interactive()){
   sampleGraph <- simpleDemoGraph()
   rcy <- RCyjs(title="getJSON", graph=sampleGraph)
   s <- getJSON(rcy)
   s.asList <- fromJSON(s)  # easier to inspect if you wish toa
   }

getLayoutStrategies

Description

getLayoutStrategies return a list of those currently offered

Usage

## S4 method for signature 'RCyjs'
getLayoutStrategies(obj)

Arguments

obj

an RCyjs instance

Value

a list of character strings

Examples

if(interactive()){
  g <- createTestGraph(nodeCount=20, edgeCount=20)
  rcy <- RCyjs(title="layouts", graph=g)
  strategies <- getLayoutStrategies(rcy)
  }

getNodeCount

Description

getNodeCount the number of nodes in the current cytoscape.js graph

Usage

## S4 method for signature 'RCyjs'
getNodeCount(obj)

Arguments

obj

RCyjs instance

Value

numeric count

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   getNodeCount(rcy)
   }

getNodes

Description

getNodes returns a data.frame, one row per node, providing id and (if present) name and label columns

Usage

## S4 method for signature 'RCyjs'
getNodes(obj, which = "all")

Arguments

obj

an RCyjs instance
which

a character string, either "all", "visible" or "hidden"

Details

Every node is guaranteed to have an "id" attribute. Becuase "name" and "label" are commonly used as well, they are returned as columns in the data.frame if present

Value

a data.frame with at least and "id" column

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   getNodes(rcy)
   }

getPosition

Description

getPosition for all or specified nodes

Usage

## S4 method for signature 'RCyjs'
getPosition(obj, nodeIDs = NA)

Arguments

obj

an RCyjs instance
nodeIDs

a vector of character strings, default NA

Value

a data.frame with "id", "x" and "y" columns

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="getPosition", graph=g)
  layout(rcy, "cose")
  tbl.pos <- getPosition(rcy)
  tbl.posA <- getPosition(rcy, "A")
  }

getSelectedNodes

Description

getSelectedNodes get the selected nodes

Usage

## S4 method for signature 'RCyjs'
getSelectedNodes(obj)

Arguments

obj

an RCyjs instance

Value

a data.frame with (at least) an id column

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   nodes.to.select <- getNodes(rcy)$id
   selectNodes(rcy, nodes.to.select)
   }

getSupportedEdgeDecoratorShapes

Description

getSupportedEdgeDecoratorShapes return a list of those currently offered

Usage

## S4 method for signature 'RCyjs'
getSupportedEdgeDecoratorShapes(obj)

Arguments

obj

an RCyjs instance

Value

a list of character strings

Examples

if(interactive()){
  g <- createTestGraph(nodeCount=20, edgeCount=20)
  rcy <- RCyjs(title="shapes", graph=g)
  shapes <- getSupportedEdgeDecoratorShapes(rcy)
  }

getSupportedNodeShapes

Description

getSupportedNodeShapes return a list of those currently offered

Usage

## S4 method for signature 'RCyjs'
getSupportedNodeShapes(obj)

Arguments

obj

an RCyjs instance

Value

a list of character strings

Examples

if(interactive()){
  g <- createTestGraph(nodeCount=20, edgeCount=20)
  rcy <- RCyjs(title="shapes", graph=g)
  shapes <- getSupportedNodeShapes(rcy)
  }

getZoom

Description

getZoom learn the zoom level of the current display

Usage

## S4 method for signature 'RCyjs'
getZoom(obj)

Arguments

obj

an RCyjs instance

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   getZoom(rcy)
   Sys.sleep(1)
   setZoom(rcy, 5)
   getZoom(rcy)
   }

Convert R graphNEL object to cytoscape.js JSON.

Description

Convert R graphNEL object to cytoscape.js JSON.

Usage

graphNELtoJSON.string(g)

Arguments

g

a graphNEL

Examples

## Not run: 
  g.json <- graphNELtoJSON.string(graphNEL())

## End(Not run)

hAlign

Description

hAlign horizontally align selected nodes

Usage

## S4 method for signature 'RCyjs'
hAlign(obj)

Arguments

obj

an RCyjs instance

Details

The shared y coordinate will be the mean of the y coordinates of selected nodes. The x coordinates are preserved.

Value

no return value

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="rcyjs demo", graph=g)
  layout(rcy, "cose")
  selectNodes(rcy, nodes(g)[1:2])
  hAlign(rcy)
  }

hideAllEdges

Description

hideAllEdges

Usage

## S4 method for signature 'RCyjs'
hideAllEdges(obj)

Arguments

obj

an RCyjs instance

Value

no return value

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="rcyjs demo", graph=g)
  layout(rcy, "cose")
  hideAllEdges()
  showAll(rcy, "edges")
  }

hideEdges

Description

hideEdges hide all edges of the specified type

Usage

## S4 method for signature 'RCyjs'
hideEdges(obj, edgeType)

Arguments

obj

an RCyjs instance
edgeType

a character string

Details

edgeType is a crucial feature for RCyjs. We assume it is an attribute found on every edge in every graph.

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   getNodes(rcy)
   edaNames(rcy)        # includes "edgeType"
   eda(rcy, "edgeType")  # includes "phosphorylates"
   hideEdges(rcy, edgeType="phosphorylates")
   showEdges(rcy, edgeType="phosphorylates")
   }

hideNodes

Description

hideNodes hide the named nodes from view

Usage

## S4 method for signature 'RCyjs'
hideNodes(obj, nodeIDs)

Arguments

obj

an RCyjs instance

Details

The hidden nodes are not deleted from the graph

Value

no return value

See Also

showAll

Examples

if(interactive()){
   g <- simpleDemoGraph()
   rcy <- RCyjs(title="rcyjs demo", graph=g)
   target <- nodes(g)[1]
   selectNodes(rcy, target)
   hideNodes(rcy)
   getNodes(rcy, "hidden")
   getNodes(rcy, "visible")
   showAll(rcy, which="nodes")
   }

hideSelectedNodes

Description

hideSelectedNodes hide selected nodes from view

Usage

## S4 method for signature 'RCyjs'
hideSelectedNodes(obj)

Arguments

obj

an RCyjs instance

Details

The hidden nodes are not deleted from the graph

Value

no return value

See Also

showAll

Examples

if(interactive()){
   g <- simpleDemoGraph()
   rcy <- RCyjs(title="rcyjs demo", graph=g)
   target <- nodes(g)[1]
   selectNodes(rcy, target)
   hideSelectedNodes(rcy)
   getNodes(rcy, "hidden")
   getNodes(rcy, "visible")
   showAll(rcy, which="nodes")
   }

invertNodeSelection

Description

invertNodeSelection deselect all selected nodes, select all previously unselected nodes

Usage

## S4 method for signature 'RCyjs'
invertNodeSelection(obj)

Arguments

obj

an RCyjs instance

Value

no return value

Examples

if(interactive()){
   g <- simpleDemoGraph()
   rcy <- RCyjs(title="rcyjs demo", graph=g)
   target <- nodes(g)[1]
   selectNodes(rcy, target)
   invertNodeSelection(rcy)
   }

layout

Description

layout apply a layout algorithm to the current grap

Usage

## S4 method for signature 'RCyjs'
layout(obj, strategy = "random")

Arguments

obj

an RCyjs instance
strategy

a character string, one of the supported algorithms

Value

explain what the method returns

See Also

getLayoutStrategies

Examples

if(interactive()){
  g <- createTestGraph(nodeCount=20, edgeCount=20)
  rcy <- RCyjs(title="layouts", graph=g)
  strategies <- getLayoutStrategies(rcy)
  for(strategy in stategies){
     layout(rcy, strategy)
     Sys.sleep(1)
     }
  }

layoutSelectionInGrid

Description

layoutSelectionInGrid arrange selected nodes in this region

Usage

## S4 method for signature 'RCyjs'
layoutSelectionInGrid(obj, x, y, w, h)

Arguments

obj

an RCyjs instance
x

numeric this will be the top left x coordinate of the grid
y

numeric the top right
w

numeric width of the grid
h

numeric height of the grid

Value

no return value

Examples

if(interactive()){
   g <- simpleDemoGraph()
   rcy <- RCyjs(title="rcyjs demo", graph=g)
   layout(rcy, "cose")
   fit(rcy, 100)
   loadStyleFile(rcy, system.file(package="RCyjs", "extdata", "sampleStyle2.js"));
   selectNodes(rcy, nodes(g))
   layoutSelectionInGrid(rcy, -1000, 10, 100, 400)
   }

layoutSelectionInGridInferAnchor

Description

layoutSelectionInGridInferAnchor the top-most, left-most of the selected nodes is the anchor

Usage

## S4 method for signature 'RCyjs'
layoutSelectionInGridInferAnchor(obj, w, h)

Arguments

obj

an RCyjs instance
w

numeric, the width of the grid box
h

numeric, the height of the grid box

Details

anchor (the top left) of the grid is the location of the topmost/leftmost node, then arrange all the selected nodes in a box anchored here.

Value

explain what the method returns

Examples

if(interactive()){
   g <- simpleDemoGraph()
   rcy <- RCyjs(title="rcyjs demo", graph=g)
   layout(rcy, "cose")
   fit(rcy, 100)
   loadStyleFile(rcy, system.file(package="RCyjs", "extdata", "sampleStyle2.js"));
   selectNodes(rcy, nodes(g))
   layoutSelectionInGrid(rcy, -1000, 10, 100, 400)
   }

loadStyleFile

Description

loadStyleFile load a named JSON cytoscape.js style file into the browser

Usage

## S4 method for signature 'RCyjs'
loadStyleFile(obj, filename)

Arguments

obj

an RCyjs instance
filename

contains json in the proper cytoscape.js format

Value

nothing

References

https://js.cytoscape.org/#style

Though we provide access to individual styling rules (see below) we often find it convenient to express all aspects of a visual style in a single JSON file

Examples

if(interactive()){
  rcy <- demo()
  filename <- system.file(package="RCyjs", "extdata", "sampleStyle1.js");
  loadStyleFile(rcy, filename)
  }

noa

Description

noa retrieve the node/attribute-value pairs, for the specified node attribute category

Usage

noa(graph, node.attribute.name)

Arguments

graph

a graphNEL
node.attribute.name

a character string

Value

character strings, the names of the unique edge attribute categories on the graph

Examples

if(interactive()){
  g <- simpleDemoGraph()
  noa(g, "lfc")
   }

noaNames

Description

noaNames the names of the unique node attribute categories on the graph (not their values)

Usage

noaNames(graph)

Arguments

graph

a graphNEL

Value

character strings, the names of the unique node attribute categories on the graph

Examples

if(interactive()){
  g <- simpleDemoGraph()
  noaNames(g)
  }

Create an RCyjs object

Description

The RCyjs class provides an R interface to cytoscape.js, a rich, interactive, full-featured, javascript network (graph) library. One constructs an RCyjs instance on a specified port (default 9000), the browser code is loaded, and a websocket connection opened.

Usage

RCyjs(
  portRange = 16000:16100,
  title = "RCyjs",
  graph = graphNEL(),
  quiet = TRUE
)

Arguments

portRange

The constructor looks for a free websocket port in this range. 16000:16100 by default
title

Used for the web browser window, "RCyjs" by default
graph

a Biocondcutor graphNEL object
quiet

A logical variable controlling verbosity during execution

Value

An object of the RCyjs class

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="rcyjs demo", graph=g)
  setNodeLabelRule(rcy, "label");
  setNodeSizeRule(rcy, "count", c(0, 30, 110), c(20, 50, 100));
  setNodeColorRule(rcy, "count", c(0, 100), c(colors$green, colors$red), mode="interpolate")
  redraw(rcy)
  layout(rcy, "cose")
  }

Read in a JSON network file, identify (or add) elements field return JSON

Description

Read in a JSON network file, identify (or add) elements field return JSON

Usage

readAndStandardizeJSONNetworkFile(filename)

Arguments

file

a json file

Read in a JSON file, extract the selector elements, return JSON

Description

Read in a JSON file, extract the selector elements, return JSON

Usage

readAndStandardizeJSONStyleFile(filename)

Arguments

file

a json file

redraw

Description

redraw re-render the graph, using the latest style rules and assignements

Usage

## S4 method for signature 'RCyjs'
redraw(obj)

Arguments

obj

an RCyjs instance

Value

explain what the method returns

Examples

if(interactive()){
   g <- simpleDemoGraph()
   rcy <- RCyjs(title="rcyjs demo", graph=g)
   layout(rcy, "cose")
   fit(rcy, 100)
   setNodeAttributes(rcy, "lfc", c("A", "B", "C"), c(0, 0, 0))
   redraw(rcy)
   }

restoreLayout

Description

restoreLayout restore a previously-saved layout

Usage

## S4 method for signature 'RCyjs'
restoreLayout(obj, filename = "layout.RData")

Arguments

obj

an RCyjs instance
filename

a character string, default "layout.RData"

Value

no return value

See Also

saveLayout

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   layout(rcy, "grid")
   saveLayout(rcy, filename="gridLayout.RData")
   layout(rcy, "circle")
   restoreLayout(rcy, "gridLayout.RData")
   }

saveJPG

Description

saveJPG write current cytoscape view, at current resolution, to a JPG file.

Usage

## S4 method for signature 'RCyjs'
saveJPG(obj, filename, resolutionFactor = 1)

Arguments

obj

an RCyjs instance
filename

a character string
resolutionFactor

numeric, default 1, higher values multiply resolution beyond screen dpi

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="layouts", graph=createTestGraph(nodeCount=20, edgeCount=20))
   style.filename <- system.file(package="RCyjs", "extdata", "sampleStyle1.js");
   loadStyleFile(rcy, style.filename)
   layout(rcy, "cose")
   fit(rcy)
   filename <- tempfile(fileext=".jpg")
   saveJPG(rcy, filename, resolutionFactor)
   }

saveLayout

Description

saveLayout to a named file

Usage

## S4 method for signature 'RCyjs'
saveLayout(obj, filename = "layout.RData")

Arguments

obj

a RCyjs instance
filename

"layout.RData" by default

Details

All node positions are saved to a functionally opaque RData object, in a file whose name you supply. These files are used by restoreLayout.

Value

no return value

See Also

restoreLayout

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   layout(rcy, "grid")
   saveLayout(rcy, filename="gridLayout.RData")
   layout(rcy, "circle")
   restoreLayout(rcy, "gridLayout.RData")
   }

savePNG

Description

savePNG write current cytoscape view, at current resolution, to a PNG file.

Usage

## S4 method for signature 'RCyjs'
savePNG(obj, filename)

Arguments

obj

an RCyjs instance
filename

a character string

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="layouts", graph=createTestGraph(nodeCount=20, edgeCount=20))
   style.filename <- system.file(package="RCyjs", "extdata", "sampleStyle1.js");
   loadStyleFile(rcy, style.filename)
   layout(rcy, "cose")
   fit(rcy)
   filename <- tempfile(fileext=".png")
   savePNG(rcy, filename)
   }

selectFirstNeighborsOfSelectedNodes

Description

selectFirstNeighborsOfSelectedNodes

Usage

## S4 method for signature 'RCyjs'
selectFirstNeighborsOfSelectedNodes(obj)

Arguments

obj

an RCyjs instance

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   selectNodes(rcy, "A")
   getSelectedNodes(rcy)  # just one
   selectFirstNeighborsOfSelectedNodes()
   getSelectedNodes(rcy)  # now three
   }

selectNodes

Description

selectNodes by node id

Usage

## S4 method for signature 'RCyjs'
selectNodes(obj, nodeIDs)

Arguments

obj

an RCyjs instance
nodeIDs

character strings

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   selectNodes(rcy, c("A", "B"))
   }

setBackgroundColor

Description

setBackgroundColor of the entire cytoscape.js div

Usage

## S4 method for signature 'RCyjs'
setBackgroundColor(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

a character string, any valid CSS color

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   setBackgroundColor(rcy, "lightblue")
   }

setDefaultEdgeColor

Description

setDefaultEdgeColor

Usage

## S4 method for signature 'RCyjs'
setDefaultEdgeColor(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

a character string, any valid CSS color

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultNodeColor", graph=g)
  layout(rcy, "cose")
  setDefaultNodeFontColor(rcy, "red")
  }

setDefaultEdgeLineColor

Description

setDefaultEdgeLineColor

Usage

## S4 method for signature 'RCyjs'
setDefaultEdgeLineColor(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

a character string, and valid CSS color

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultEdgeLineColor", graph=g)
  layout(rcy, "cose")
  setDefaultEdgeLineColor(rcy, "red")
  }

setDefaultEdgeLineStyle

Description

setDefaultEdgeLineStyle put somewhat more detailed description here

Usage

## S4 method for signature 'RCyjs'
setDefaultEdgeLineStyle(obj, newValue = c("solid", "dotted", "dashed"))

Arguments

obj

an RCyjs instance
newValue

a character string, one of "solid", "dotted", or "dashed"

Details

multi-line description goes here with continuations on subsequent lines if you like

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultEdgeLineStyle", graph=g)
  layout(rcy, "cose")
  setDefaultEdgeLineColor(rcy, "dashed")
  }

setDefaultEdgeSourceArrowColor

Description

setDefaultEdgeSourceArrowColor

Usage

## S4 method for signature 'RCyjs'
setDefaultEdgeSourceArrowColor(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

a character string, and valid CSS color

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultEdgeSourceArrowColor", graph=g)
  layout(rcy, "cose")
  setDefaultEdgeSourceArrowColor(rcy, "red")
  }

setDefaultEdgeSourceArrowShape

Description

setDefaultEdgeSourceArrowShape put somewhat more detailed description here

Usage

## S4 method for signature 'RCyjs'
setDefaultEdgeSourceArrowShape(
  obj,
  newValue = c("triangle", "triangle-tee", "triangle-cross", "triangle-backcurve", "vee",
    "tee", "square", "circle", "diamond", "none")
)

Arguments

obj

an RCyjs instance
newValue

a character string, one of "triangle", "triangle-tee", "triangle-cross", "triangle-backcurve", "vee", "tee", "square", "circle", "diamond", "none"

Details

multi-line description goes here with continuations on subsequent lines if you like

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultEdgeSourceArrowShape", graph=g)
  layout(rcy, "cose")
  setDefaultEdgeSourceArrowShape(rcy, "tee")
  }

setDefaultEdgeTargetArrowColor

Description

setDefaultEdgeTargetArrowColor

Usage

## S4 method for signature 'RCyjs'
setDefaultEdgeTargetArrowColor(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

a character string, and valid CSS color

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultEdgeTargetArrowColor", graph=g)
  layout(rcy, "cose")
  setDefaultEdgeTargetArrowColor(rcy, "red")
  }

setDefaultEdgeTargetArrowShape

Description

setDefaultEdgeTargetArrowShape put somewhat more detailed description here

Usage

## S4 method for signature 'RCyjs'
setDefaultEdgeTargetArrowShape(
  obj,
  newValue = c("triangle", "triangle-tee", "triangle-cross", "triangle-backcurve", "vee",
    "tee", "square", "circle", "diamond", "none")
)

Arguments

obj

an RCyjs instance
newValue

a character string, one of "triangle", "triangle-tee", "triangle-cross", "triangle-backcurve", "vee", "tee", "square", "circle", "diamond", "none"

Details

multi-line description goes here with continuations on subsequent lines if you like

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultEdgeTargetArrowShape", graph=g)
  layout(rcy, "cose")
  setDefaultEdgeTargetArrowShape(rcy, "tee")
  }

setDefaultEdgeWidth

Description

setDefaultEdgeWidth in pixels

Usage

## S4 method for signature 'RCyjs'
setDefaultEdgeWidth(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

a numeric

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultEdgeWidth", graph=g)
  layout(rcy, "cose")
  setDefaultEdgeWidth(rcy, 1)
  }

setDefaultNodeBorderColor

Description

setDefaultNodeBorderColor put somewhat more detailed description here

Usage

## S4 method for signature 'RCyjs'
setDefaultNodeBorderColor(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

any CSS color

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultNodeBorderColor", graph=g)
  layout(rcy, "cose")
  setDefaultNodeBorderColor(rcy, "red")
  }

setDefaultNodeBorderWidth

Description

setDefaultNodeBorderWidth in pixels

Usage

## S4 method for signature 'RCyjs'
setDefaultNodeBorderWidth(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

numeric, in pixels

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultNodeBorderWidth", graph=g)
  layout(rcy, "cose")
  setDefaultNodeBorderWidth(rcy, 2)
  }

setDefaultNodeColor

Description

setDefaultNodeColor put somewhat more detailed description here

Usage

## S4 method for signature 'RCyjs'
setDefaultNodeColor(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

a character string, any valid CSS color name

Details

multi-line description goes here with continuations on subsequent lines if you like

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultNodeColor", graph=g)
  layout(rcy, "cose")
  setDefaultNodeColor(rcy, "lightblue")
  }

setDefaultNodeFontColor

Description

setDefaultNodeFontColor

Usage

## S4 method for signature 'RCyjs'
setDefaultNodeFontColor(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

any CSS color

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultNodeColor", graph=g)
  layout(rcy, "cose")
  setDefaultNodeFontColor(rcy, "red")
  }

setDefaultNodeFontSize

Description

setDefaultNodeFontSize put somewhat more detailed description here

Usage

## S4 method for signature 'RCyjs'
setDefaultNodeFontSize(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

numeric, in points

Details

multi-line description goes here with continuations on subsequent lines if you like

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultNodeFontSize", graph=g)
  layout(rcy, "cose")
  setDefaultNodeFontSize(rcy, 8)
  }

setDefaultNodeHeight

Description

setDefaultNodeHeight set all nodes to the same specifed width, in pixels

Usage

## S4 method for signature 'RCyjs'
setDefaultNodeHeight(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

a numeric, in pixels

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultNodeHeight", graph=g)
  layout(rcy, "cose")
  setDefaultNodeHeight(rcy, 80)
  }

setDefaultNodeShape

Description

setDefaultNodeShape change the shape of all nodes

Usage

## S4 method for signature 'RCyjs'
setDefaultNodeShape(
  obj,
  newValue = c("ellipse", "triangle", "rectangle", "roundrectangle",
    "bottomroundrectangle", "cutrectangle", "barrel", "rhomboid", "diamond", "pentagon",
    "hexagon", "concavehexagon", "heptagon", "octagon", "star", "tag", "vee")
)

Arguments

obj

an RCyjs instance
newValue

a character string, one of "ellipse", "triangle", "rectangle", "roundrectangle", "bottomroundrectangle","cutrectangle", "barrel", "rhomboid", "diamond", "pentagon", "hexagon", "concavehexagon", "heptagon", "octagon", "star", "tag", "vee"

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultNodeShape", graph=g)
  layout(rcy, "cose")
  setDefaultNodeShape(rcy, "barrel")
  }

setDefaultNodeSize

Description

setDefaultNodeSize set all nodes to the same specifed size, in pixels

Usage

## S4 method for signature 'RCyjs'
setDefaultNodeSize(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

a numeric, in pixels

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultNodesSize", graph=g)
  layout(rcy, "cose")
  setDefaultNodeSize(rcy, 80)
  }

setDefaultNodeWidth

Description

setDefaultNodeWidth set all nodes to the same specifed width, in pixels

Usage

## S4 method for signature 'RCyjs'
setDefaultNodeWidth(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

a numeric, in pixels

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultNodesWidth", graph=g)
  layout(rcy, "cose")
  setDefaultNodeWidth(rcy, 80)
  }

setDefaultStyle

Description

setDefaultStyle use some sensible rendering options for all elements of the graph

Usage

## S4 method for signature 'RCyjs'
setDefaultStyle(obj)

Arguments

obj

an RCyjs instance

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setDefaultNodesSize", graph=g)
  layout(rcy, "cose")
  setDefaultStyle(rcy)
  }

setEdgeAttributes

Description

setEdgeAttributes on the graph in the browse

Usage

## S4 method for signature 'RCyjs'
setEdgeAttributes(obj, attribute, sourceNodes, targetNodes, edgeTypes, values)

Arguments

obj

an RCyjs instance
attribute

a character string
sourceNodes

vector of character strings
targetNodes

vector of character strings
edgeTypes

vector of character strings
values

vector of character strings

Details

Edges are specified by sourceNode/targetNode/edgeType triples.

Value

no return value

setEdgeStyle

Description

setEdgeStyle plain & fast (haystack) vs fancy & slower (bezier)

Usage

## S4 method for signature 'RCyjs'
setEdgeStyle(obj, mode = c("bezier", "haystack"))

Arguments

obj

an RCyjs instance
mode

a character string, either "bezier" or "haystack"

Details

cytoscape.js offers two kinds of edge rendering - a tradeoff in richess and speed edge target decorations (arrows, tee, etc) are only rendered with the "bezier" style

Value

no return value

Examples

if(interactive()){
   g <- simpleDemoGraph()
   rcy <- RCyjs(title="rcyjs demo", graph=g)
   layout(rcy, "cose")
   fit(rcy, 100)
   loadStyleFile(rcy, system.file(package="RCyjs", "extdata", "sampleStyle2.js"))
   setEdgeStyle(rcy, "bezier")
   redraw(rcy)
   }

setGraph

Description

setGraph Establish a new graph in RCyjs, removing any previous graph

Usage

## S4 method for signature 'RCyjs'
setGraph(obj, graph)

Arguments

obj

RCyjs instance
graph

a graphNEL

Details

This method will remove any previous graph in the browser, adding a new one. Setting visual properties and performing layout must follow.

Value

nothing

See Also

addGraph

Examples

if(interactive()){
  sampleGraph <- simpleDemoGraph()
  rcy <- RCyjs(title="rcyjs demo")
  setGraph(rcy, sampleGraph)
  }

setNodeAttributes

Description

setNodeAttributes put somewhat more detailed description here

Usage

## S4 method for signature 'RCyjs'
setNodeAttributes(obj, attribute, nodes, values)

Arguments

obj

an RCyjs instance
attribute

a character string
nodes

character strings - node ids
values

scalar values, all of one type (all numeric, or all character, or all integer, ...)

Details

multi-line description goes here with continuations on subsequent lines if you like

Value

explain what the method returns

Examples

if(interactive()){
   g <- simpleDemoGraph()
   rcy <- RCyjs(title="rcyjs demo", graph=g)
   layout(rcy, "cose")
   fit(rcy, 100)
   setNodeAttributes(rcy, "lfc", c("A", "B", "C"), c(0, 0, 0))
   redraw(rcy)
   }

setNodeBorderColor

Description

setNodeBorderColor set the specified nodes to the specifed node border color

Usage

## S4 method for signature 'RCyjs'
setNodeBorderColor(obj, nodeIDs, newValues)

Arguments

obj

an RCyjs instance
nodeIDs

a character string (one or more)
newValues

legal CSS color names (one or more)

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setNodeBorderColor", graph=g)
  layout(rcy, "cose")
  setNodeBorderColor(rcy, "green")
  }

setNodeBorderWidth

Description

setNodeBorderWidth set the specified nodes to the same specifed node border width, in pixels

Usage

## S4 method for signature 'RCyjs'
setNodeBorderWidth(obj, nodeIDs, newValues)

Arguments

obj

an RCyjs instance
nodeIDs

a character string (one or more)
newValues

numeric, in pixels (one, or as many as there are nodeIDs)

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setNodeBorderWidth", graph=g)
  layout(rcy, "cose")
  setNodeBorderWidth(rcy, 3)
  }

setNodeColor

Description

setNodeColor set the specified nodes to the specifed color

Usage

## S4 method for signature 'RCyjs'
setNodeColor(obj, nodeIDs, newValues)

Arguments

obj

an RCyjs instance
nodeIDs

a character string (one or more)
newValues

a character string, legal CSS color names (one or more)

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setNodeColor", graph=g)
  layout(rcy, "cose")
  setNodeColor(rcy, 80)
  }

setNodeColorRule

Description

setNodeColorRule control node color via values of the specified attribute

Usage

## S4 method for signature 'RCyjs'
setNodeColorRule(
  obj,
  attribute,
  control.points,
  colors,
  mode = c("interpolate", "lookup")
)

Arguments

obj

an RCyjs instance
attribute

a character string, the node attribute category whose value controls color
control.points

a list of all possible values of the attribute
colors

the corresponding node color, one specified for each of the control.points
mode

a character string, either "interpolate" or "lookup"

Details

for interpolate mode, in which the node attribute should be a continusously varying numerical quantity in-between colors are calculated for in-between values. for lookup mode, in which the node attribute is a discrete string variable, simple color lookup is performed.

Value

no return value

Examples

if(interactive()){
   g <- simpleDemoGraph()
   rcy <- RCyjs(title="rcyjs demo", graph=g)
   layout(rcy, "cose")
   fit(rcy, 100)
   setNodeColorRule(rcy, "count", c(0, 100), c("green", "red"), mode="interpolate")
   redraw(rcy)
   }

setNodeFontColor

Description

setNodeFontColor set the specified nodes to the same specifed node font color

Usage

## S4 method for signature 'RCyjs'
setNodeFontColor(obj, nodeIDs, newValues)

Arguments

obj

an RCyjs instance
nodeIDs

a character string (one or more)
newValues

a character string, a legal CSS color name (one or more)

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setNodeFontColor", graph=g)
  layout(rcy, "cose")
  setNodeFontColor(rcy, "red")
  }

setNodeFontSize

Description

setNodeFontSize set the specified nodes to the same specifed node font size

Usage

## S4 method for signature 'RCyjs'
setNodeFontSize(obj, nodeIDs, newValues)

Arguments

obj

an RCyjs instance
nodeIDs

a character string (one or more)
newValues

a numeric, in pixels (one, or as many as there are nodeIDs)

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setNodeFontSize", graph=g)
  layout(rcy, "cose")
  setNodeFontSize(rcy, 5)
  }

setNodeHeight

Description

setNodeHeight set the specified nodes to the specifed heights, in pixels

Usage

## S4 method for signature 'RCyjs'
setNodeHeight(obj, nodeIDs, newValues)

Arguments

obj

an RCyjs instance
nodeIDs

a character string (one or more)
newValues

a numeric, in pixels (one, or as many as there are nodeIDs)

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setNodesHeight", graph=g)
  layout(rcy, "cose")
  setNodeHeight(rcy, 80)
  }

setNodelLabelAlignment

Description

setNodeLabelAlignment put somewhat more detailed description here

Usage

## S4 method for signature 'RCyjs'
setNodeLabelAlignment(obj, horizontal, vertical)

Arguments

obj

an RCyjs instance
horizontal

character string
vertical

character string

Details

multi-line description goes here with continuations on subsequent lines if you like

Value

explain what the method returns

setNodeLabelRule

Description

setNodeLabelRule put somewhat more detailed description here

Usage

## S4 method for signature 'RCyjs'
setNodeLabelRule(obj, attribute)

Arguments

obj

an RCyjs instance
attribute

a character string, the node attribute to display as label

Details

multi-line description goes here with continuations on subsequent lines if you like

Value

explain what the method returns

Examples

if(interactive()){
  g <- createTestGraph(nodeCount=20, edgeCount=20)
  rcy <- RCyjs(title="layouts", graph=g)
  setNodeLabelRule(rcy, "label");
  }

setNodeShape

Description

setNodeShape set the specified nodes to specifed shapes

Usage

## S4 method for signature 'RCyjs'
setNodeShape(obj, nodeIDs, newValues)

Arguments

obj

an RCyjs instance
nodeIDs

a character string (one or more)
newValues

a character string, one of the legitimate cytoscape.js node shapes

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setNodeShape", graph=g)
  layout(rcy, "cose")
  setNodeShape(rcy, 80)
  }

setNodeSize

Description

setNodeSize set the specified nodes to the specifed sizes, in pixels

Usage

## S4 method for signature 'RCyjs'
setNodeSize(obj, nodeIDs, newValues)

Arguments

obj

an RCyjs instance
nodeIDs

a character string (one or more)
newValues

a numeric, in pixels (one, or as many as there are nodeIDs)

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setNodesSize", graph=g)
  layout(rcy, "cose")
  setNodeSize(rcy, 80)
  }

setNodeSizeRule

Description

setNodeSizeRule control node size via values of the specified attribute

Usage

## S4 method for signature 'RCyjs'
setNodeSizeRule(obj, attribute, control.points, node.sizes)

Arguments

obj

an RCyjs instance
attribute

a character string, the node attribute category whose value controls size
control.points

a list of values of the attribute
node.sizes

the corresponding node size, one specified for each of the control.points

Details

actual node sizes are interpolated via the specified relationship of control.points node.sizes

Value

no return value

Examples

if(interactive()){
   g <- simpleDemoGraph()
   rcy <- RCyjs(title="rcyjs demo", graph=g)
   layout(rcy, "cose")
   fit(rcy, 100)
   setNodeSizeRule(rcy, "count", c(0, 30, 110), c(20, 50, 100));
   redraw(rcy)
   }

setNodeWidth

Description

setNodeWidth set the specified nodes to the specifed widths, in pixels

Usage

## S4 method for signature 'RCyjs'
setNodeWidth(obj, nodeIDs, newValues)

Arguments

obj

an RCyjs instance
nodeIDs

a character string (one or more)
newValues

a numeric, in pixels (one, or as many as there are nodeIDs)

Value

no value returned

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="setNodesWidth", graph=g)
  layout(rcy, "cose")
  setNodeWidth(rcy, 80)
  }

setPosition

Description

setPosition of nodes by their id

Usage

## S4 method for signature 'RCyjs'
setPosition(obj, tbl.pos)

Arguments

obj

an RCyjs instance
tbl.pos

a data.frame with three columns: id, x, y

Value

no return value

See Also

getPosition

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="getPosition", graph=g)
  layout(rcy, "cose")
  tbl.pos <- getPosition(rcy)
    # shift all the nodes to the right
  tbl.pos$x <- tbl.pos$x + 50
  setPosition(rcy, tbl.pos)
  }

setZoom

Description

setZoom zoom in or out

Usage

## S4 method for signature 'RCyjs'
setZoom(obj, newValue)

Arguments

obj

an RCyjs instance
newValue

numeric, typically be 0.1 (zoomed way out, nodes are small) and 10 (zoomed way in, nodes are large)

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   setZoom(rcy, 0.2)
   Sys.sleep(1)
   setZoom(rcy, 5)
   }

sfn

Description

sfn select first neighbors of the currently selected nodes

Usage

## S4 method for signature 'RCyjs'
sfn(obj)

Arguments

obj

an RCyjs instance

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   selectNodes(rcy, "A")
   getSelectedNodes(rcy)  # just one
   sfn()
   getSelectedNodes(rcy)  # now three
   }

showAll

Description

showAll show any hidden objects: nodes, edges, or both

Usage

## S4 method for signature 'RCyjs'
showAll(obj, which = c("both", "nodes", "edges"))

Arguments

obj

an RCyjs instance
which

a character string, either "nodes", "edges" or "both"

Value

no return value

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="rcyjs demo", graph=g)
  layout(rcy, "cose")
  selectNodes(rcy, getNodes(rcy)$id)
  hideSelectedNodes(rcy)
  showAll(rcy, "nodes")
  }

showEdges

Description

showEdges if hidden, edges of the specified type will be made visible

Usage

## S4 method for signature 'RCyjs'
showEdges(obj, edgeType)

Arguments

obj

an RCyjs instance
edgeType

a character string

Details

edgeType is a crucial feature for RCyjs. We assume it is an attribute found on every edge in every graph.

Value

no return value

Examples

if(interactive()){
   rcy <- RCyjs(title="rcyjs demo", graph=simpleDemoGraph())
   getNodes(rcy)
   edaNames(rcy)        # includes "edgeType"
   eda(rcy, "edgeType")  # includes "phosphorylates"
   hideEdges(rcy, edgeType="phosphorylates")
   showEdges(rcy, edgeType="phosphorylates")
   }

showNodes

Description

showNodes show the named nodes from view

Usage

## S4 method for signature 'RCyjs'
showNodes(obj, nodeIDs)

Arguments

obj

an RCyjs instance

Value

no return value

See Also

showAll

Examples

if(interactive()){
   g <- simpleDemoGraph()
   rcy <- RCyjs(title="rcyjs demo", graph=g)
   target <- nodes(g)[1]
   hideNodes(rcy, "A")
   getNodes(rcy, "hidden")
   getNodes(rcy, "visible")
   showNodes(rcy, "A")
   getNodes(rcy, "visible")
   }

simpleDemoGraph

Description

simpleDemoGraph

Usage

simpleDemoGraph()

Value

a graphNEL with 3 nodes and 3 edges

Examples

g <- simpleDemoGraph()

vAlign

Description

vAlign vertically align selected nodes

Usage

## S4 method for signature 'RCyjs'
vAlign(obj)

Arguments

obj

an RCyjs instance

Details

The shared x coordinate will be the mean of the x coordinates of selected nodes. The y coordinates are preserved.

Value

no return value

Examples

if(interactive()){
  g <- simpleDemoGraph()
  rcy <- RCyjs(title="rcyjs demo", graph=g)
  layout(rcy, "cose")
  selectNodes(rcy, nodes(g)[1:2])
  vAlign(rcy)
  }