| Title: | Cytoscape.js Shiny Widget (cyjShiny) |
| Version: | 1.0.42 |
| Date: | 2023-03-28 |
| Description: | Wraps cytoscape.js as a shiny widget. cytoscape.js https://js.cytoscape.org/ is a Javascript-based graph theory (network) library for visualization and analysis. This package supports the visualization of networks with custom visual styles and several available layouts. Demo Shiny applications are provided in the package code. |
| Depends: | R (≥ 3.5.0), htmlwidgets, shiny, jsonlite, graph, base64enc |
| Suggests: | RUnit, knitr, rmarkdown, markdown, BiocStyle |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| LazyData: | false |
| Collate: | 'graphsToJSON.R' 'cyjShiny.R' |
| VignetteBuilder: | knitr |
| RoxygenNote: | 7.2.0 |
| NeedsCompilation: | no |
| Packaged: | 2023-03-28 19:15:32 UTC; user |
| Author: | Omar Shah [ctb],
Paul Shannon [aut],
Augustin Luna 
[aut, cre] |
| Maintainer: | Augustin Luna <augustin_luna@hms.harvard.edu> |
| Repository: | CRAN |
| Date/Publication: | 2023-03-28 21:00:02 UTC |
Add graph from data.frame
Description
Add graph from data.frame
Usage
addGraphFromDataFrame(session, tbl.edges, tbl.nodes = NULL)
Arguments
session |
a Shiny Server session object. |
tbl.edges |
a data.frame with source, traget, interaction columns (and option other attributes) |
tbl.nodes |
(optional; nodes can be deduced from tbl.edges) a data.frame with nodes and their attributes |
Value
Nothing
Examples
## Not run:
addGraphFromDataFrame(session)
## End(Not run)
Add graph from JSON file
Description
Add graph from JSON file
Usage
addGraphFromJsonFile(session, jsonFilename)
Arguments
session |
a Shiny Server session object. |
jsonFilename |
of a text file with JSON representation of a cytoscape.js graph |
Value
Nothing
Examples
## Not run:
addGraphFromJsonFile(session)
## End(Not run)
Clear selection all node and edge selections removed
Description
Clear selection all node and edge selections removed
Usage
clearSelection(session)
Arguments
session |
a Shiny Server session object. |
Value
Nothing
cyjShiny cyjShiny
Description
This widget wraps cytoscape.js, a full-featured Javsscript network library for visualization and analysis.
Usage
cyjShiny(
graph,
layoutName,
styleFile = NULL,
width = NULL,
height = NULL,
elementId = NULL
)
Arguments
graph |
a graph in json format; converters from graphNEL and data.frame/s offered ("see also" below) |
layoutName |
character one of:"preset", "cose", "cola", "circle", "concentric", "breadthfirst", "grid", "random" |
styleFile |
default NULL, can name a standard javascript cytoscape.js style file |
width |
integer initial width of the widget. |
height |
integer initial height of the widget. |
elementId |
string the DOM id into which the widget is rendered, default NULL is best. |
Value
a reference to an htmlwidget.
See Also
Examples
tbl.nodes <- data.frame(
id = c("A", "B", "C"),
type = c("kinase", "TF", "glycoprotein"),
lfc = c(-3, 1, 1),
count = c(0, 0, 0),
stringsAsFactors = FALSE
)
tbl.edges <- data.frame(
source = c("A", "B", "C"),
target = c("B", "C", "A"),
interaction = c("phosphorylates", "synthetic lethal", "unknown"),
stringsAsFactors = FALSE
)
# simple legitimate graph, nodes implied, but no node attributes
graph.json.v1 <- dataFramesToJSON(tbl.edges)
# nodes and edges both explicit, attributes specified
graph.json.v2 <- dataFramesToJSON(tbl.edges, tbl.nodes)
g <- graphNEL(nodes = c("A", "B", "C"), edgemode = "directed")
g <- addEdge("A", "B", g)
graph.json.v3 <- graphNELtoJSON(g)
# output$cyjShiny <- renderCyjShiny(cyjShiny(graph.json.v[123]))
Standard shiny ui rendering construct
Description
Standard shiny ui rendering construct
Usage
cyjShinyOutput(outputId, width = "100%", height = "400")
Arguments
outputId |
the name of the DOM element to create. |
width |
integer optional initial width of the widget. |
height |
integer optional initial height of the widget. |
Value
a reference to an htmlwidget
Examples
## Not run:
mainPanel(cyjShinyOutput("cyjShiny"), width = 10)
## End(Not run)
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 |
Value
a string with a cytoscape.js JSON graph
Layout the current graph using the specified strategy.
Description
Layout the current graph using the specified strategy.
Usage
doLayout(session, strategy)
Arguments
session |
a Shiny Server session object. |
strategy |
a character string, one of cola, cose, circle, concentric, grid, breadthfirst, random, dagre, cose-bilkent. |
Value
Nothing
Examples
## Not run:
doLayout(session, "cola")
## End(Not run)
Set zoom and center of the graph display so that graph fills the display.
Description
Set zoom and center of the graph display so that graph fills the display.
Usage
fit(session, padding = 50)
Arguments
session |
a Shiny server session object. |
padding |
integer, default 50 pixels. |
Value
Nothing
See Also
Examples
## Not run:
fit(session, 100)
## End(Not run)
Set zoom and center of the graph display so that the currently selected nodes fill the display
Description
Set zoom and center of the graph display so that the currently selected nodes fill the display
Usage
fitSelected(session, padding = 50)
Arguments
session |
a Shiny server session object. |
padding |
integer, default 50 pixels. |
Value
Nothing
See Also
Examples
## Not run:
fitSelected(session, 100)
## End(Not run)
Get node positions
Description
Get node positions
Usage
getNodePositions(session)
Arguments
session |
a Shiny Server session object. |
Value
Nothing
Get Selected Nodes
Description
Get Selected Nodes
Usage
getSelectedNodes(session)
Arguments
session |
a Shiny server session object. |
Value
a data.frame with (at least) an id column
getSelectedNodes get the selected nodes
Convert R graphNEL object to cytoscape.js JSON.
Description
Convert R graphNEL object to cytoscape.js JSON.
Usage
graphNELtoJSON(g)
Arguments
g |
a graphNEL |
Value
a string with a cytoscape.js JSON graph
Examples
## Not run:
g.json <- graphNELtoJSON(graphNEL())
## End(Not run)
Hide selection all selected nodes and their edges are hidden
Description
Hide selection all selected nodes and their edges are hidden
Usage
hideSelection(session)
Arguments
session |
a Shiny Server session object. |
Value
Nothing
Invert selection all selected nodes and their edges are hidden
Description
Invert selection all selected nodes and their edges are hidden
Usage
invertSelection(session)
Arguments
session |
a Shiny Server session object. |
Value
Nothing
Load a standard cytoscape.js JSON network file
Description
Load a standard cytoscape.js JSON network file
Usage
loadNetworkFromJSONFile(filename)
Arguments
filename |
character string, either relative or absolute path. |
Value
Nothing
Examples
## Not run:
loadNetworkFromJSONFile(system.file(package = "cyjShiny", "extdata", "galFiltered.cyjs"))
## End(Not run)
Load a standard cytoscape.js style file
Description
Load a standard cytoscape.js style file
Usage
loadStyleFile(styleFile)
Arguments
styleFile |
character string, either relative or absolute path. |
Value
Nothing
Examples
## Not run:
loadStyleFile(system.file(package = "cyjShiny", "extdata", "yeastGalactoseStyle.js"))
## End(Not run)
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
filename |
a JSON file |
Value
a string with a cytoscape.js JSON graph
Read in a JSON file, extract the selector elements, return JSON
Description
this utility function examines the incoming JSON, returns exactly and only an array of selector objects
Usage
readAndStandardizeJSONStyleFile(filename)
Arguments
filename |
a json file |
Details
there are at least two JSON object structures used to specify style (see function comments in code for more details):
simple: an array of selector objects
more complex, exported from the Cytoscape desktop application this is also an array of objects, one named "style" which (like the simple format described above) contains an array of selectors.
Value
a string with a cytoscape.js JSON graph
Remove the current graph
Description
Remove the current graph
Usage
removeGraph(session)
Arguments
session |
a Shiny Server session object. |
Value
Nothing
Examples
## Not run:
removeGraph(session)
## End(Not run)
More shiny plumbing - a cyjShiny wrapper for htmlwidget standard rendering operation
Description
More shiny plumbing - a cyjShiny wrapper for htmlwidget standard rendering operation
Usage
renderCyjShiny(expr, env = parent.frame(), quoted = FALSE)
Arguments
expr |
an expression that generates an HTML widget. |
env |
environment in which to evaluate expr. |
quoted |
logical specifies whether expr is quoted ("useuful if you want to save an expression in a variable"). |
Value
output from htmlwidgets rendering operation
Save a png rendering of the current network view to the specified filename
Description
Save a png rendering of the current network view to the specified filename
Usage
savePNGtoFile(session, filename)
Arguments
session |
a Shiny Server session object. |
filename |
a character string |
Value
Nothing
Select first neighbors of the currently selected nodes
Description
Select first neighbors of the currently selected nodes
Usage
selectFirstNeighbors(session)
Arguments
session |
a Shiny Server session object. |
Value
Nothing
Select Nodes
Description
Select Nodes
Usage
selectNodes(session, nodeNames)
Arguments
session |
a Shiny Server session object. |
nodeNames |
character, a list of node IDs |
Value
Nothing
Assign the supplied edge attribute values to the graph structure contained in the browser.
Description
Assign the supplied edge attribute values to the graph structure contained in the browser.
Usage
setEdgeAttributes(
session,
attributeName,
sourceNodes,
targetNodes,
interactions,
values
)
Arguments
session |
a Shiny Server session object. |
attributeName |
character string, the attribute to update. |
sourceNodes |
a character vector, the names of the source nodes of the edges |
targetNodes |
a character vector, the names of the target nodes of the edgees |
interactions |
a character vector, further identifying the specific edge whose attributes are updated. |
values |
a character, logical or numeric vector, the new values. |
Value
Nothing
Examples
## Not run:
setEdgeAttributes(session,
attributeName = "score",
sourceNodes = c("A", "B", "C"),
targetNodes = c("D", "E", "A"),
interactions = c("promotes", "promotes", "inhibits"),
values = new.scores
)
## End(Not run)
Assign the supplied node attribute values to the graph structure contained in the browser.
Description
Assign the supplied node attribute values to the graph structure contained in the browser.
Usage
setNodeAttributes(session, attributeName, nodes, values)
Arguments
session |
a Shiny Server session object. |
attributeName |
character string, the attribute to update. |
nodes |
a character vector the names of the nodes whose attributes are updated. |
values |
a character, logical or numeric vector, the new values. |
Value
Nothing
Examples
## Not run:
setNodeAttributes(session,
attributeName = attribute,
nodes = yeastGalactodeNodeIDs,
values = expression.vector
)
## End(Not run)
Set node positions from the supplied data.frame
Description
Set node positions from the supplied data.frame
Usage
setNodePositions(session, tbl.positions)
Arguments
session |
a Shiny Server session object. |
tbl.positions |
a data.frame with three columns: id, x, y |
Value
Nothing
Show all all selected nodes and their edges are hidden
Description
Show all all selected nodes and their edges are hidden
Usage
showAll(session)
Arguments
session |
a Shiny Server session object. |
Value
Nothing