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Convert one of numerous data types to tree_network's 'native' treenetdf form

Source: R/as_tree_data.R
as_tree_data.Rd

The tree_network function uses a 'native' data format that consists of a data frame with minimally 2 vectors/columns, one named 'nodeId' and one named 'parentId'. Other columns in the data frame are also passed on to the JavaScript code and attached to the elements in the D3 visualization so that they can potentially be accessed by other JavaScript functions. This is an advantageous format because:

  • it's an easy to use and understand R-like format

  • a hierarchical network can be succinctly defined by a list of each unique node and its parent node

  • since each row defines a unique node, additional columns can be added to add node-specific properties

  • in a hierarchical network, every link/edge can be uniquely identified by the node which it leads to, therefore each link/edge can also be specifically addressed by adding columns for formatting of the incoming link

as_tree_data can convert from any of the following data types:

  • leafpathdf (table)–parent|parent|node–data.frame

  • hierarchical nested list (JSON)

  • hclust

  • data.tree Node

  • igraph

  • ape phylo

Usage

as_tree_data(data, ...)

# S3 method for class 'character'
as_tree_data(data, ...)

# S3 method for class 'hclust'
as_tree_data(data, ...)

# S3 method for class 'list'
as_tree_data(data, children_name = "children", node_name = "name", ...)

# S3 method for class 'Node'
as_tree_data(data, ...)

# S3 method for class 'phylo'
as_tree_data(data, ...)

# S3 method for class 'tbl_graph'
as_tree_data(data, ...)

# S3 method for class 'igraph'
as_tree_data(data, root = "root", ...)

# S3 method for class 'data.frame'
as_tree_data(
  data,
  cols = NULL,
  df_type = "treenetdf",
  subset = names(data),
  root,
  ...
)

Arguments

data

a tree network description in one of numerous forms (see details).

...

other arguments that will be passed on to as_tree_data

children_name

character specifying the name used for the list element that contains the childeren elements.

node_name

character specifying the name used for the list element that contains the name of the node

root

root name.

cols

named character vector specifying the names of columns to be converted to the standard treenetdf names.

df_type

character specifying which type of data frame to convert. Can be treenetdf or leafpathdf.

subset

character vector specifying the names of the columns (in order) that should be used to define the hierarchy.

Methods (by class)

  • as_tree_data(character): Convert JSON from URL to treenetdf

  • as_tree_data(hclust): Convert hclust objects to treenetdf

  • as_tree_data(list): Convert a nested list to treenetdf

  • as_tree_data(Node): data.tree to treenetdf

  • as_tree_data(phylo): Phylo tree to treenetdf

  • as_tree_data(tbl_graph): tbl_graph_to_treenetdf

  • as_tree_data(igraph): Convert igraph tree to treenetdf

  • as_tree_data(data.frame): Convert a data.frame to a treenetdf

Examples

links <- read.csv(header = TRUE, stringsAsFactors = FALSE, text = '
                   source,target,name
                   1,,one
                   2,1,two
                   3,1,three
                   4,1,four
                   5,2,five
                   6,2,six
                   7,2,seven
                   8,6,eight')

 # Convert data
 as_tree_data(links, cols = c(nodeId = 'source', parentId = 'target'))
#> # A tibble: 8 × 3
#>   nodeId parentId name 
#>    <int>    <int> <chr>
#> 1      1       NA one  
#> 2      2        1 two  
#> 3      3        1 three
#> 4      4        1 four 
#> 5      5        2 five 
#> 6      6        2 six  
#> 7      7        2 seven
#> 8      8        6 eight