Help for package collapsibleTree

Type:

Package

Title:

Interactive Collapsible Tree Diagrams using 'D3.js'

Version:

0.1.8

Maintainer:

Adeel Khan <AdeelK@gwu.edu>

Description:

Interactive Reingold-Tilford tree diagrams created using 'D3.js', where every node can be expanded and collapsed by clicking on it. Tooltips and color gradients can be mapped to nodes using a numeric column in the source data frame. See 'collapsibleTree' website for more information and examples.

License:

GPL (≥ 3)

URL:

https://github.com/AdeelK93/collapsibleTree, https://AdeelK93.github.io/collapsibleTree/

BugReports:

https://github.com/AdeelK93/collapsibleTree/issues

Encoding:

UTF-8

Depends:

R (≥ 3.0.0)

Imports:

htmlwidgets, data.tree, stats, methods

Enhances:

knitr, shiny

RoxygenNote:

7.2.3

Suggests:

colorspace, RColorBrewer, dplyr, testthat, tibble

NeedsCompilation:

Packaged:

2023-11-13 05:25:03 UTC; Adeel

Author:

Adeel Khan [aut, cre], Dhrumin Shah [ctb], Mike Bostock [ctb, cph] (D3.js library, http://d3js.org)

Repository:

CRAN

Date/Publication:

2023-11-13 05:53:23 UTC

Create Interactive Collapsible Tree Diagrams

Description

Interactive Reingold-Tilford tree diagram created using D3.js, where every node can be expanded and collapsed by clicking on it.

Usage

collapsibleTree(
  df,
  ...,
  inputId = NULL,
  attribute = "leafCount",
  aggFun = sum,
  fill = "lightsteelblue",
  linkLength = NULL,
  fontSize = 10,
  tooltip = FALSE,
  tooltipHtml = NULL,
  nodeSize = NULL,
  collapsed = TRUE,
  zoomable = TRUE,
  width = NULL,
  height = NULL
)

## S3 method for class 'data.frame'
collapsibleTree(
  df,
  hierarchy,
  root = deparse(substitute(df)),
  inputId = NULL,
  attribute = "leafCount",
  aggFun = sum,
  fill = "lightsteelblue",
  fillByLevel = TRUE,
  linkLength = NULL,
  fontSize = 10,
  tooltip = FALSE,
  nodeSize = NULL,
  collapsed = TRUE,
  zoomable = TRUE,
  width = NULL,
  height = NULL,
  ...
)

## S3 method for class 'Node'
collapsibleTree(
  df,
  hierarchy_attribute = "level",
  root = df$name,
  inputId = NULL,
  attribute = "leafCount",
  aggFun = sum,
  fill = "lightsteelblue",
  linkLength = NULL,
  fontSize = 10,
  tooltip = FALSE,
  tooltipHtml = NULL,
  nodeSize = NULL,
  collapsed = TRUE,
  zoomable = TRUE,
  width = NULL,
  height = NULL,
  ...
)

Arguments

df

a data.frame from which to construct a nested list (where every row is a leaf) or a preconstructed data.tree

...

other arguments to pass onto S3 methods that implement this generic function - collapsibleTree.data.frame, collapsibleTree.Node

inputId

the input slot that will be used to access the selected node (for Shiny). Will return a named list of the most recently clicked node, along with all of its parents.

attribute

numeric column not listed in hierarchy that will be used for tooltips, if applicable. Defaults to 'leafCount', which is the cumulative count of a node's children

aggFun

aggregation function applied to the attribute column to determine values of parent nodes. Defaults to sum, but mean also makes sense.

fill

either a single color or a mapping of colors:

For data.frame input, a vector of colors the same length as the number of nodes. By default, vector should be ordered by level, such that the root color is described first, then all the children's colors, and then all the grandchildren's colors
For data.tree input, a tree attribute containing the color for each node

linkLength

length of the horizontal links that connect nodes in pixels. (optional, defaults to automatic sizing)

fontSize

font size of the label text in pixels

tooltip shows the node's label and attribute value.

tooltipHtml

column name (possibly containing html) to override default tooltip contents, allowing for more advanced customization. Applicable only for data.tree input.

nodeSize

numeric column that will be used to determine relative node size. Default is to have a constant node size throughout. 'leafCount' can also be used here (cumulative count of a node's children), or 'count' (count of node's immediate children).

collapsed

the tree's children will start collapsed by default

For data.frame input, can also be a vector of logical values the same length as the number of nodes. Follows the same logic as the fill vector.
For data.tree input, can also be a tree attribute for conditionally collapsing nodes

zoomable

pan and zoom by dragging and scrolling

width

width in pixels (optional, defaults to automatic sizing)

height

height in pixels (optional, defaults to automatic sizing)

hierarchy

a character vector of column names that define the order and hierarchy of the tree network. Applicable only for data.frame input.

root

label for the root node

fillByLevel

which order to assign fill values to nodes. TRUE: Filling by level; will assign fill values to nodes vertically. FALSE: Filling by order; will assign fill values to nodes horizontally.

hierarchy_attribute

name of the data.tree attribute that contains hierarchy information of the tree network. Applicable only for data.tree input.

Source

Christopher Gandrud: http://christophergandrud.github.io/networkD3/.

d3noob: https://bl.ocks.org/d3noob/43a860bc0024792f8803bba8ca0d5ecd.

Examples

collapsibleTree(warpbreaks, c("wool", "tension", "breaks"))

# Data from US Forest Service DataMart
species <- read.csv(system.file("extdata/species.csv", package = "collapsibleTree"))
collapsibleTree(df = species, c("REGION", "CLASS", "NAME"), fill = "green")

# Visualizing the order in which the node colors are filled
library(RColorBrewer)
collapsibleTree(
  warpbreaks, c("wool", "tension"),
  fill = brewer.pal(9, "RdBu"),
  fillByLevel = TRUE
)
collapsibleTree(
  warpbreaks, c("wool", "tension"),
  fill = brewer.pal(9, "RdBu"),
  fillByLevel = FALSE
)

# Tooltip can be mapped to an attribute, or default to leafCount
collapsibleTree(
  warpbreaks, c("wool", "tension", "breaks"),
  tooltip = TRUE,
  attribute = "breaks"
)

# Node size can be mapped to any numeric column, or to leafCount
collapsibleTree(
  warpbreaks, c("wool", "tension", "breaks"),
  nodeSize = "breaks"
)

# collapsibleTree.Node example
data(acme, package="data.tree")
acme$Do(function(node) node$cost <- data.tree::Aggregate(node, attribute = "cost", aggFun = sum))
acme$Do(function(node) node$lessThanMillion <- node$cost < 10^6)
collapsibleTree(
  acme,
  nodeSize  = "cost",
  attribute = "cost",
  tooltip = TRUE,
  collapsed = "lessThanMillion"
)

# Emulating collapsibleTree.data.frame using collapsibleTree.Node
species <- read.csv(system.file("extdata/species.csv", package = "collapsibleTree"))
hierarchy <- c("REGION", "CLASS", "NAME")
species$pathString <- paste(
  "species",
  apply(species[,hierarchy], 1, paste, collapse = "//"),
  sep = "//"
)
df <- data.tree::as.Node(species, pathDelimiter = "//")
collapsibleTree(df)

Shiny bindings for collapsibleTree

Description

Output and render functions for using collapsibleTree within Shiny applications and interactive Rmd documents.

Usage

collapsibleTreeOutput(outputId, width = "100%", height = "400px")

renderCollapsibleTree(expr, env = parent.frame(), quoted = FALSE)

Arguments

outputId

output variable to read from

width, height

Must be a valid CSS unit (like '100%', '400px', 'auto') or a number, which will be coerced to a string and have 'px' appended.

expr

An expression that generates a collapsibleTree

env

The environment in which to evaluate expr.

quoted

Is expr a quoted expression (with quote())? This is useful if you want to save an expression in a variable.

Examples

if(interactive()) {

  # Shiny Interaction
  shiny::runApp(system.file("examples/02shiny", package = "collapsibleTree"))

  # Interactive Gradient Mapping
  shiny::runApp(system.file("examples/03shiny", package = "collapsibleTree"))

}

Create Network Interactive Collapsible Tree Diagrams

Description

Interactive Reingold-Tilford tree diagram created using D3.js, where every node can be expanded and collapsed by clicking on it. This function serves as a convenience wrapper for network style data frames containing the node's parent in the first column, node parent in the second column, and additional attributes in the rest of the columns. The root node is denoted by having an NA for a parent. There must be exactly 1 root.

Usage

collapsibleTreeNetwork(
  df,
  inputId = NULL,
  attribute = "leafCount",
  aggFun = sum,
  fill = "lightsteelblue",
  linkLength = NULL,
  fontSize = 10,
  tooltip = TRUE,
  tooltipHtml = NULL,
  nodeSize = NULL,
  collapsed = TRUE,
  zoomable = TRUE,
  width = NULL,
  height = NULL
)

Arguments

df

a network data frame (where every row is a node) from which to construct a nested list

First column must be the parent (NA for root node)
Second column must be the child
Additional columns are passed on as attributes for other parameters
There must be exactly 1 root node

inputId

the input slot that will be used to access the selected node (for Shiny). Will return a named list of the most recently clicked node, along with all of its parents. (For collapsibleTreeNetwork the names of the list are tree depth)

attribute

numeric column not listed in hierarchy that will be used as weighting to define the color gradient across nodes. Defaults to 'leafCount', which colors nodes by the cumulative count of its children

aggFun

aggregation function applied to the attribute column to determine values of parent nodes. Defaults to sum, but mean also makes sense.

fill

either a single color or a column name with the color for each node

linkLength

length of the horizontal links that connect nodes in pixels. (optional, defaults to automatic sizing)

fontSize

font size of the label text in pixels

tooltip shows the node's label and attribute value.

tooltipHtml

column name (possibly containing html) to override default tooltip contents, allowing for more advanced customization

nodeSize

collapsed

the tree's children will start collapsed by default. Can also be a logical value found in the data for conditionally collapsing nodes.

zoomable

pan and zoom by dragging and scrolling

width

width in pixels (optional, defaults to automatic sizing)

height

height in pixels (optional, defaults to automatic sizing)

Source

Christopher Gandrud: http://christophergandrud.github.io/networkD3/.

d3noob: https://bl.ocks.org/d3noob/43a860bc0024792f8803bba8ca0d5ecd.

Examples

# Create a simple org chart
org <- data.frame(
  Manager = c(
    NA, "Ana", "Ana", "Bill", "Bill", "Bill", "Claudette", "Claudette", "Danny",
    "Fred", "Fred", "Grace", "Larry", "Larry", "Nicholas", "Nicholas"
  ),
  Employee = c(
    "Ana", "Bill", "Larry", "Claudette", "Danny", "Erika", "Fred", "Grace",
    "Henri", "Ida", "Joaquin", "Kate", "Mindy", "Nicholas", "Odette", "Peter"
  ),
  Title = c(
    "President", "VP Operations", "VP Finance", "Director", "Director", "Scientist",
    "Manager", "Manager", "Jr Scientist", "Operator", "Operator", "Associate",
     "Analyst", "Director", "Accountant", "Accountant"
  )
)
collapsibleTreeNetwork(org, attribute = "Title")

# Add in colors and sizes
org$Color <- org$Title
levels(org$Color) <- colorspace::rainbow_hcl(11)
collapsibleTreeNetwork(
  org,
  attribute = "Title",
  fill = "Color",
  nodeSize = "leafCount",
  collapsed = FALSE
)

# Use unsplash api to add in random photos to tooltip
org$tooltip <- paste0(
  org$Employee,
  "<br>Title: ",
  org$Title,
  "<br><img src='https://source.unsplash.com/collection/385548/150x100'>"
)

collapsibleTreeNetwork(
  org,
  attribute = "Title",
  fill = "Color",
  nodeSize = "leafCount",
  tooltipHtml = "tooltip",
  collapsed = FALSE
)

Create Summary Interactive Collapsible Tree Diagrams

Description

Interactive Reingold-Tilford tree diagram created using D3.js, where every node can be expanded and collapsed by clicking on it. This function serves as a convenience wrapper to add color gradients to nodes either by counting that node's children (default) or specifying another numeric column in the input data frame.

Usage

collapsibleTreeSummary(
  df,
  hierarchy,
  root = deparse(substitute(df)),
  inputId = NULL,
  attribute = "leafCount",
  fillFun = colorspace::heat_hcl,
  maxPercent = 25,
  percentOfParent = FALSE,
  linkLength = NULL,
  fontSize = 10,
  tooltip = TRUE,
  nodeSize = NULL,
  collapsed = TRUE,
  zoomable = TRUE,
  width = NULL,
  height = NULL,
  ...
)

Arguments

df

a data frame (where every row is a leaf) from which to construct a nested list

hierarchy

a character vector of column names that define the order and hierarchy of the tree network

root

label for the root node

inputId

the input slot that will be used to access the selected node (for Shiny). Will return a named list of the most recently clicked node, along with all of its parents.

attribute

numeric column not listed in hierarchy that will be used as weighting to define the color gradient across nodes. Defaults to 'leafCount', which colors nodes by the cumulative count of its children

fillFun

function that takes its first argument and returns a vector of colors of that length. rainbow_hcl is a good example.

maxPercent

highest weighting percent to use in color scale mapping. All numbers above this value will be treated as the same maximum value for the sake of coloring in the nodes (but not the ordering of nodes). Setting this value too high will make it difficult to tell the difference between nodes with many children.

percentOfParent

toggle attribute tooltip to be percent of parent rather than the actual value of attribute

linkLength

length of the horizontal links that connect nodes in pixels. (optional, defaults to automatic sizing)

fontSize

font size of the label text in pixels

tooltip shows the node's label and attribute value.

nodeSize

collapsed

the tree's children will start collapsed by default (There is no conditional collapsing in this function yet, but it could be implemented if there's sufficient demand)

zoomable

pan and zoom by dragging and scrolling

width

width in pixels (optional, defaults to automatic sizing)

height

height in pixels (optional, defaults to automatic sizing)

...

other arguments passed on to fillFun, such declaring a palette for brewer.pal

Source

Christopher Gandrud: http://christophergandrud.github.io/networkD3/.

d3noob: https://bl.ocks.org/d3noob/43a860bc0024792f8803bba8ca0d5ecd.

Examples

# Color in by number of children
collapsibleTreeSummary(warpbreaks, c("wool", "tension", "breaks"), maxPercent = 50)

# Color in by the value of breaks and use the terrain_hcl gradient
collapsibleTreeSummary(
  warpbreaks,
  c("wool", "tension", "breaks"),
  attribute = "breaks",
  fillFun = colorspace::terrain_hcl,
  maxPercent = 50
)

Create Interactive Collapsible Tree Diagrams

Description

Usage

Arguments

Source

Examples

Shiny bindings for collapsibleTree

Description

Usage

Arguments

Examples

Create Network Interactive Collapsible Tree Diagrams

Description

Usage

Arguments

Source

See Also

Examples

Create Summary Interactive Collapsible Tree Diagrams

Description

Usage

Arguments

Source

Examples