Create Interactive Collapsible Tree Diagrams

Source: R/collapsibleTree.R, R/collapsibleTree.data.frame.R, R/collapsibleTree.data.tree.R

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

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

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.

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)