Title: Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R
Description: This packages is intended to make it easy to create D3 JavaScript network, tree, dendrogram, and Sankey graphs from R using data frames. !!! NOTE: Active development has moved to the networkD3 package. !!!
Version: 0.5.2.1
Date: 2015-01-31
Author: Christopher Gandrud
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
URL: http://christophergandrud.github.io/d3Network/
BugReports: https://github.com/christophergandrud/d3Network/issues
License: GPL (≥ 3)
Depends: R (≥ 3.0.0)
Imports: plyr, rjson, whisker
Suggests: RCurl
Packaged: 2015-01-31 12:08:44 UTC; christophergandrud
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-31 17:29:42

Read a link-node structured JSON file into R as two data frames.

Description

JSONtoDF reads a JSON data file into R and converts part of it to a data frame.

Usage

JSONtoDF(jsonStr = NULL, file = NULL, array)

Arguments

jsonStr

a JSON object to convert. Note if jsonStr is specified, then file must be NULL.

file

character string of the JSON file name. Note if file is specified, then jsonStr must be NULL.

array

character string specifying the name of the JSON array to extract. (JSON arrays are delimited by square brackets).

Details

JSONtoDF is intended to load JSON files into R and convert them to data frames that can be used to create network graphs. The command converts the files into R lists and then extracts the JSON array the user would like to make into a data frame.

Source

Part of the idea for the command comes from mropa's comment on StackExchange: http://stackoverflow.com/questions/4227223/r-list-to-data-frame.

Description

A data file of links from Knuth's Les Miserables characters data base.

Format

A data set with 254 observations of 3 variables.

Source

See Mike Bostock http://bl.ocks.org/mbostock/4062045.

A data file of nodes from Knuth's Les Miserables characters data base.

Description

A data file of nodes from Knuth's Les Miserables characters data base.

Format

A data set with 77 observations of 2 variables.

Source

See Mike Bostock http://bl.ocks.org/mbostock/4062045.

Create a D3 JavaScript Cluster Dendrogram graphs.

Description

Create a D3 JavaScript Cluster Dendrogram graphs.

Usage

d3ClusterDendro(List, height = 2200, width = 900, heightCollapse = 0,
  widthCollapse = 0.5, fontsize = 10, linkColour = "#ccc",
  nodeColour = "#3182bd", textColour = "#3182bd", opacity = 0.8,
  diameter = 980, zoom = FALSE, parentElement = "body",
  standAlone = TRUE, file = NULL, iframe = FALSE,
  d3Script = "http://d3js.org/d3.v3.min.js")

Arguments

List

a hierarchical list object with a root node and children.

height

numeric height for the network graph's frame area in pixels.

width

numeric width for the network graph's frame area in pixels.

heightCollapse

numeric proportion of the overall graph height to make the cluster dendrogram shorter by.

widthCollapse

numeric proportion of the overall graph width to make the cluster dendrogram narrower by.

fontsize

numeric font size in pixels for the node text labels.

linkColour

character string specifying the colour you want the link lines to be. Multiple formats supported (e.g. hexadecimal).

nodeColour

character string specifying the colour you want the node circles to be. Multiple formats supported (e.g. hexadecimal).

textColour

character string specifying the colour you want the text to be before they are clicked. Multiple formats supported (e.g. hexadecimal).

opacity

numeric value of the proportion opaque you would like the graph elements to be.

diameter

numeric diameter for the network in pixels.

zoom

logical, whether or not to enable the ability to use the mouse scroll-wheel to zoom in and out of the graph.

parentElement

character string specifying the parent element for the resulting svg network graph. This effectively allows the user to specify where on the html page the graph will be placed. By default the parent element is body.

standAlone

logical, whether or not to return a complete HTML document (with head and foot) or just the script.

file

a character string of the file name to save the resulting graph. If a file name is given a standalone webpage is created, i.e. with a header and footer. If file = NULL then result is returned to the console.

iframe

logical. If iframe = TRUE then the graph is saved to an external file in the working directory and an HTML iframe linking to the file is printed to the console. This is useful if you are using Slidify and many other HTML slideshow framworks and want to include the graph in the resulting page. If you set the knitr code chunk results='asis' then the graph will be rendered in the output. Usually, you can use iframe = FALSE if you are creating simple knitr Markdown or HTML pages. Note: you do not need to specify the file name if iframe = TRUE, however if you do, do not include the file path.

d3Script

a character string that allows you to specify the location of the d3.js script you would like to use. The default is http://d3js.org/d3.v3.min.js.

Source

Mike Bostock http://bl.ocks.org/mbostock/4063570.

Examples

## Not run: 
# Download JSON data
library(RCurl)
URL <- "https://raw.github.com/christophergandrud/d3Network/master/JSONdata/flare.json"
Flare <- getURL(URL)

# Convert to list format
Flare <- rjson::fromJSON(Flare)

# Recreate Bostock example from http://bl.ocks.org/mbostock/4063570
d3ClusterDendro(List = Flare,
					file = "FlareCluster.html", zoom = TRUE,
     			fontsize = 10, opacity = 0.9,
     			widthCollapse = 0.8)

## End(Not run)

Create a D3 JavaScript force directed network graph.

Description

Create a D3 JavaScript force directed network graph.

Usage

d3ForceNetwork(Links, Nodes, Source, Target, Value = NULL, NodeID, Group,
  height = 600, width = 900, fontsize = 7, linkDistance = 50,
  linkWidth = "function(d) { return Math.sqrt(d.value); }", charge = -120,
  linkColour = "#666", opacity = 0.6, zoom = FALSE,
  parentElement = "body", standAlone = TRUE, file = NULL,
  iframe = FALSE, d3Script = "http://d3js.org/d3.v3.min.js")

Arguments

Links

a data frame object with the links between the nodes. It should include the Source and Target for each link. These should be numbered starting from 0. An optional Value variable can be included to specify how close the nodes are to one another.

Nodes

a data frame containing the node id and properties of the nodes. If no ID is specified then the nodes must be in the same order as the Source variable column in the Links data frame. Currently only a grouping variable is allowed.

Source

character string naming the network source variable in the Links data frame.

Target

character string naming the network target variable in the Links data frame.

Value

character string naming the variable in the Links data frame for how wide the links are.

NodeID

character string specifying the node IDs in the Nodes data frame.

Group

character string specifying the group of each node in the Nodes data frame.

height

numeric height for the network graph's frame area in pixels.

width

numeric width for the network graph's frame area in pixels.

fontsize

numeric font size in pixels for the node text labels.

linkDistance

numeric or character string. Either numberic fixed distance between the links in pixels (actually arbitrary relative to the diagram's size). Or a JavaScript function, possibly to weight by Value. For example: linkDistance = "function(d){return d.value * 10}".

linkWidth

numeric or character string. Can be a numeric fixed width in pixels (arbitrary relative to the diagram's size). Or a JavaScript function, possibly to weight by Value. The default is linkWidth = "function(d) { return Math.sqrt(d.value); }".

charge

numeric value indicating either the strength of the node repulsion (negative value) or attraction (positive value).

linkColour

character string specifying the colour you want the link lines to be. Multiple formats supported (e.g. hexadecimal).

opacity

numeric value of the proportion opaque you would like the graph elements to be.

zoom

logical, whether or not to enable the ability to use the mouse scroll-wheel to zoom in and out of the graph.

parentElement

character string specifying the parent element for the resulting svg network graph. This effectively allows the user to specify where on the html page the graph will be placed. By default the parent element is body.

standAlone

logical, whether or not to return a complete HTML document (with head and foot) or just the script.

file

a character string of the file name to save the resulting graph. If a file name is given a standalone webpage is created, i.e. with a header and footer. If file = NULL then result is returned to the console.

iframe

logical. If iframe = TRUE then the graph is saved to an external file in the working directory and an HTML iframe linking to the file is printed to the console. This is useful if you are using Slidify and many other HTML slideshow framworks and want to include the graph in the resulting page. If you set the knitr code chunk results='asis' then the graph will be rendered in the output. Usually, you can use iframe = FALSE if you are creating simple knitr Markdown or HTML pages. Note: you do not need to specify the file name if iframe = TRUE, however if you do, do not include the file path.

d3Script

a character string that allows you to specify the location of the d3.js script you would like to use. The default is http://d3js.org/d3.v3.min.js.

Source

D3.js was created by Michael Bostock. See http://d3js.org/ and, more specifically for force directed networks https://github.com/mbostock/d3/wiki/Force-Layout.

Examples

#### Tabular data example.
# Load data
data(MisLinks)
data(MisNodes)

# Create graph
d3ForceNetwork(Links = MisLinks, Nodes = MisNodes, Source = "source",
               Target = "target", Value = "value", NodeID = "name",
               Group = "group", opacity = 0.4)

## Not run: 
#### JSON Data Example
# Load data JSON formated data into two R data frames
library(RCurl)
MisJson <- getURL("http://bit.ly/1cc3anB")
MisLinks <- JSONtoDF(jsonStr = MisJson, array = "links")
MisNodes <- JSONtoDF(jsonStr = MisJson, array = "nodes")

# Create graph
d3ForceNetwork(Links = MisLinks, Nodes = MisNodes, Source = "source",
               Target = "target", Value = "value", NodeID = "name",
               Group = "group", opacity = 0.4)

## End(Not run)

Function for creating simple D3 JavaScript force directed network graphs. DEPRICATED, USE d3SimpleNetwork

Description

d3Network creates D3 JavaScript force directed network graphs. NOTE: it is depricated. It is currently a direct copy of d3SimpleNetwork

Usage

d3Network(Data, Source = NULL, Target = NULL, height = 600, width = 900,
  fontsize = 7, linkDistance = 50, charge = -200, linkColour = "#666",
  nodeColour = "#3182bd", nodeClickColour = "#E34A33",
  textColour = "#3182bd", opacity = 0.6, parentElement = "body",
  standAlone = TRUE, file = NULL, iframe = FALSE,
  d3Script = "http://d3js.org/d3.v3.min.js")

Arguments

Data

a data frame object with three columns. The first two are the names of the linked units. The third records an edge value. (Currently the third column doesn't affect the graph.)

Source

character string naming the network source variable in the data frame. If Source = NULL then the first column of the data frame is treated as the source.

Target

character string naming the network target variable in the data frame. If Target = NULL then the second column of the data frame is treated as the target.

height

numeric height for the network graph's frame area in pixels.

width

numeric width for the network graph's frame area in pixels.

fontsize

numeric font size in pixels for the node text labels.

linkDistance

numeric distance between the links in pixels (actually arbitrary relative to the diagram's size).

charge

numeric value indicating either the strength of the node repulsion (negative value) or attraction (positive value).

linkColour

character string specifying the colour you want the link lines to be. Multiple formats supported (e.g. hexadecimal).

nodeColour

character string specifying the colour you want the node circles to be. Multiple formats supported (e.g. hexadecimal).

nodeClickColour

character string specifying the colour you want the node circles to be when they are clicked. Also changes the colour of the text. Multiple formats supported (e.g. hexadecimal).

textColour

character string specifying the colour you want the text to be before they are clicked. Multiple formats supported (e.g. hexadecimal).

opacity

numeric value of the proportion opaque you would like the graph elements to be.

parentElement

character string specifying the parent element for the resulting svg network graph. This effectively allows the user to specify where on the html page the graph will be placed. By default the parent element is body.

standAlone

logical, whether or not to return a complete HTML document (with head and foot) or just the script.

file

a character string of the file name to save the resulting graph. If a file name is given a standalone webpage is created, i.e. with a header and footer. If file = NULL then result is returned to the console.

iframe

logical. If iframe = TRUE then the graph is saved to an external file in the working directory and an HTML iframe linking to the file is printed to the console. This is useful if you are using Slidify and many other HTML slideshow framworks and want to include the graph in the resulting page. If you set the knitr code chunk results='asis' then the graph will be rendered in the output. Usually, you can use iframe = FALSE if you are creating simple knitr Markdown or HTML pages. Note: you do not need to specify the file name if iframe = TRUE, however if you do, do not include the file path.

d3Script

a character string that allows you to specify the location of the d3.js script you would like to use. The default is http://d3js.org/d3.v3.min.js.

Source

D3.js was created by Michael Bostock. See http://d3js.org/ and, more specifically for directed networks https://github.com/mbostock/d3/wiki/Force-Layout

Create a D3 JavaScript Sankey diagram

Description

Create a D3 JavaScript Sankey diagram

Usage

d3Sankey(Links, Nodes, Source, Target, Value = NULL, NodeID, height = 600,
  width = 900, fontsize = 7, nodeWidth = 15, nodePadding = 10,
  parentElement = "body", standAlone = TRUE, file = NULL,
  iframe = FALSE, d3Script = "http://d3js.org/d3.v3.min.js")

Arguments

Links

a data frame object with the links between the nodes. It should have include the Source and Target for each link. An optional Value variable can be included to specify how close the nodes are to one another.

Nodes

a data frame containing the node id and properties of the nodes. If no ID is specified then the nodes must be in the same order as the Source variable column in the Links data frame. Currently only grouping variable is allowed.

Source

character string naming the network source variable in the Links data frame.

Target

character string naming the network target variable in the Links data frame.

Value

character string naming the variable in the Links data frame for how far away the nodes are from one another.

NodeID

character string specifying the node IDs in the Nodes data frame.

height

numeric height for the network graph's frame area in pixels.

width

numeric width for the network graph's frame area in pixels.

fontsize

numeric font size in pixels for the node text labels.

nodeWidth

numeric width of each node.

nodePadding

numeric essentially influences the width height.

parentElement

character string specifying the parent element for the resulting svg network graph. This effectively allows the user to specify where on the html page the graph will be placed. By default the parent element is body.

standAlone

logical, whether or not to return a complete HTML document (with head and foot) or just the script.

file

a character string of the file name to save the resulting graph. If a file name is given a standalone webpage is created, i.e. with a header and footer. If file = NULL then result is returned to the console.

iframe

logical. If iframe = TRUE then the graph is saved to an external file in the working directory and an HTML iframe linking to the file is printed to the console. This is useful if you are using Slidify and many other HTML slideshow framworks and want to include the graph in the resulting page. If you set the knitr code chunk results='asis' then the graph will be rendered in the output. Usually, you can use iframe = FALSE if you are creating simple knitr Markdown or HTML pages. Note: you do not need to specify the file name if iframe = TRUE, however if you do, do not include the file path.

d3Script

a character string that allows you to specify the location of the d3.js script you would like to use. The default is http://d3js.org/d3.v3.min.js.

Source

D3.js was created by Michael Bostock. See http://d3js.org/ and, more specifically for Sankey diagrams http://bost.ocks.org/mike/sankey/.

Examples

## Not run: 
# Recreate Bostock Sankey diagram: http://bost.ocks.org/mike/sankey/
# Load energy projection data
library(RCurl)
URL <- "https://raw.githubusercontent.com/christophergandrud/d3Network/sankey/JSONdata/energy.json"
Energy <- getURL(URL, ssl.verifypeer = FALSE)
# Convert to data frame
EngLinks <- JSONtoDF(jsonStr = Energy, array = "links")
EngNodes <- JSONtoDF(jsonStr = Energy, array = "nodes")

# Plot
d3Sankey(Links = EngLinks, Nodes = EngNodes, Source = "source",
         Target = "target", Value = "value", NodeID = "name",
         fontsize = 12, nodeWidth = 30, file = "~/Desktop/TestSankey.html")

## End(Not run)

Function for creating simple D3 JavaScript force directed network graphs.

Description

d3SimpleNetwork creates simple D3 JavaScript force directed network graphs.

Usage

d3SimpleNetwork(Data, Source = NULL, Target = NULL, height = 600,
  width = 900, fontsize = 7, linkDistance = 50, charge = -200,
  linkColour = "#666", nodeColour = "#3182bd",
  nodeClickColour = "#E34A33", textColour = "#3182bd", opacity = 0.6,
  parentElement = "body", standAlone = TRUE, file = NULL,
  iframe = FALSE, d3Script = "http://d3js.org/d3.v3.min.js")

Arguments

Data

a data frame object with three columns. The first two are the names of the linked units. The third records an edge value. (Currently the third column doesn't affect the graph.)

Source

character string naming the network source variable in the data frame. If Source = NULL then the first column of the data frame is treated as the source.

Target

character string naming the network target variable in the data frame. If Target = NULL then the second column of the data frame is treated as the target.

height

numeric height for the network graph's frame area in pixels.

width

numeric width for the network graph's frame area in pixels.

fontsize

numeric font size in pixels for the node text labels.

linkDistance

numeric distance between the links in pixels (actually arbitrary relative to the diagram's size).

charge

numeric value indicating either the strength of the node repulsion (negative value) or attraction (positive value).

linkColour

character string specifying the colour you want the link lines to be. Multiple formats supported (e.g. hexadecimal).

nodeColour

character string specifying the colour you want the node circles to be. Multiple formats supported (e.g. hexadecimal).

nodeClickColour

character string specifying the colour you want the node circles to be when they are clicked. Also changes the colour of the text. Multiple formats supported (e.g. hexadecimal).

textColour

character string specifying the colour you want the text to be before they are clicked. Multiple formats supported (e.g. hexadecimal).

opacity

numeric value of the proportion opaque you would like the graph elements to be.

parentElement

character string specifying the parent element for the resulting svg network graph. This effectively allows the user to specify where on the html page the graph will be placed. By default the parent element is body.

standAlone

logical, whether or not to return a complete HTML document (with head and foot) or just the script.

file

a character string of the file name to save the resulting graph. If a file name is given a standalone webpage is created, i.e. with a header and footer. If file = NULL then result is returned to the console.

iframe

logical. If iframe = TRUE then the graph is saved to an external file in the working directory and an HTML iframe linking to the file is printed to the console. This is useful if you are using Slidify and many other HTML slideshow framworks and want to include the graph in the resulting page. If you set the knitr code chunk results='asis' then the graph will be rendered in the output. Usually, you can use iframe = FALSE if you are creating simple knitr Markdown or HTML pages. Note: you do not need to specify the file name if iframe = TRUE, however if you do, do not include the file path.

d3Script

a character string that allows you to specify the location of the d3.js script you would like to use. The default is http://d3js.org/d3.v3.min.js.

Source

D3.js was created by Michael Bostock. See http://d3js.org/ and, more specifically for directed networks https://github.com/mbostock/d3/wiki/Force-Layout

Examples

# Fake data
Source <- c("A", "A", "A", "A", "B", "B", "C", "C", "D")
Target <- c("B", "C", "D", "J", "E", "F", "G", "H", "I")
NetworkData <- data.frame(Source, Target)

# Create graph
d3SimpleNetwork(NetworkData, height = 300, width = 700,
                 fontsize = 15)

Creates a D3 JavaScript Reingold-Tilford Tree network graph.

Description

Creates a D3 JavaScript Reingold-Tilford Tree network graph.

Usage

d3Tree(List, height = 600, width = 900, fontsize = 10,
  linkColour = "#ccc", nodeColour = "#3182bd", textColour = "#3182bd",
  opacity = 0.9, diameter = 980, zoom = FALSE, parentElement = "body",
  standAlone = TRUE, file = NULL, iframe = FALSE,
  d3Script = "http://d3js.org/d3.v3.min.js")

Arguments

List

a hierarchical list object with a root node and children.

height

numeric height for the network graph's frame area in pixels.

width

numeric width for the network graph's frame area in pixels.

fontsize

numeric font size in pixels for the node text labels.

linkColour

character string specifying the colour you want the link lines to be. Multiple formats supported (e.g. hexadecimal).

nodeColour

character string specifying the colour you want the node circles to be. Multiple formats supported (e.g. hexadecimal).

textColour

character string specifying the colour you want the text to be before they are clicked. Multiple formats supported (e.g. hexadecimal).

opacity

numeric value of the proportion opaque you would like the graph elements to be.

diameter

numeric diameter for the network in pixels.

zoom

logical, whether or not to enable the ability to use the mouse scroll-wheel to zoom in and out of the graph.

parentElement

character string specifying the parent element for the resulting svg network graph. This effectively allows the user to specify where on the html page the graph will be placed. By default the parent element is body.

standAlone

logical, whether or not to return a complete HTML document (with head and foot) or just the script.

file

a character string of the file name to save the resulting graph. If a file name is given a standalone webpage is created, i.e. with a header and footer. If file = NULL then result is returned to the console.

iframe

logical. If iframe = TRUE then the graph is saved to an external file in the working directory and an HTML iframe linking to the file is printed to the console. This is useful if you are using Slidify and many other HTML slideshow framworks and want to include the graph in the resulting page. If you set the knitr code chunk results='asis' then the graph will be rendered in the output. Usually, you can use iframe = FALSE if you are creating simple knitr Markdown or HTML pages. Note: you do not need to specify the file name if iframe = TRUE, however if you do, do not include the file path.

d3Script

a character string that allows you to specify the location of the d3.js script you would like to use. The default is http://d3js.org/d3.v3.min.js.

Source

Reingold. E. M., and Tilford, J. S. (1981). Tidier Drawings of Trees. IEEE Transactions on Software Engineering, SE-7(2), 223-228.

Mike Bostock: http://bl.ocks.org/mbostock/4063550.

Examples

## Create tree from R list
# Create hierarchical list
CanadaPC <- list(name = "Canada", children = list(list(name = "Newfoundland",
                    children = list(list(name = "St. John's"))),
               list(name = "PEI",
                    children = list(list(name = "Charlottetown"))),
               list(name = "Nova Scotia",
                    children = list(list(name = "Halifax"))),
               list(name = "New Brunswick",
                    children = list(list(name = "Fredericton"))),
               list(name = "Quebec",
                    children = list(list(name = "Montreal"),
                                    list(name = "Quebec City"))),
               list(name = "Ontario",
                    children = list(list(name = "Toronto"),
                                    list(name = "Ottawa"))),
               list(name = "Manitoba",
                    children = list(list(name = "Winnipeg"))),
               list(name = "Saskatchewan",
                    children = list(list(name = "Regina"))),
               list(name = "Nunavuet",
                    children = list(list(name = "Iqaluit"))),
               list(name = "NWT",
                    children = list(list(name = "Yellowknife"))),
               list(name = "Alberta",
                    children = list(list(name = "Edmonton"))),
               list(name = "British Columbia",
                    children = list(list(name = "Victoria"),
                                    list(name = "Vancouver"))),
               list(name = "Yukon",
                    children = list(list(name = "Whitehorse")))
))

# Create tree
d3Tree(List = CanadaPC, fontsize = 10, diameter = 500)

## Create tree from JSON formatted data
## dontrun
## Download JSON data
# library(RCurl)
# URL <- "https://raw.github.com/christophergandrud/d3Network/master/JSONdata/flare.json"
# Flare <- getURL(URL)

## Convert to list format
# Flare <- rjson::fromJSON(Flare)

## Recreate Bostock example from http://bl.ocks.org/mbostock/4063550
# d3Tree(List = Flare, file = "Flare.html",
#        fontsize = 10, opacity = 0.9, diameter = 1000)

JSON data file of a projection of UK energy production and consumption in 2050.

Description

JSON data file of a projection of UK energy production and consumption in 2050.

Format

A JSON file with two arrays nodes and links.

Source

See Mike Bostock http://bost.ocks.org/mike/sankey/.

JSON data file of the Flare class hierarchy.

Description

JSON data file of the Flare class hierarchy.

Format

A JSON file with two arrays name and children.

Source

See Mike Bostock http://bl.ocks.org/mbostock/4063550.