tbl_graph: A data structure for tidy graph manipulation

In tidygraph: A Tidy API for Graph Manipulation

A data structure for tidy graph manipulation

Description

The tbl_graph class is a thin wrapper around an igraph object that provides methods for manipulating the graph using the tidy API. As it is just a subclass of igraph every igraph method will work as expected. A grouped_tbl_graph is the equivalent of a grouped_df where either the nodes or the edges has been grouped. The grouped_tbl_graph is not constructed directly but by using the group_by() verb. After creation of a tbl_graph the nodes are activated by default. The context can be changed using the activate() verb and affects all subsequent operations. Changing context automatically drops any grouping. The current active context can always be extracted with as_tibble(), which drops the graph structure and just returns a tbl_df or a grouped_df depending on the state of the tbl_graph. The returned context can be overriden by using the active argument in as_tibble().

Usage

## S3 method for class 'data.frame'
as_tbl_graph(x, directed = TRUE, ...)

## S3 method for class 'Node'
as_tbl_graph(x, directed = TRUE, mode = "out", ...)

## S3 method for class 'dendrogram'
as_tbl_graph(x, directed = TRUE, mode = "out", ...)

## S3 method for class 'graphNEL'
as_tbl_graph(x, ...)

## S3 method for class 'graphAM'
as_tbl_graph(x, ...)

## S3 method for class 'graphBAM'
as_tbl_graph(x, ...)

## S3 method for class 'hclust'
as_tbl_graph(x, directed = TRUE, mode = "out", ...)

## S3 method for class 'igraph'
as_tbl_graph(x, ...)

## S3 method for class 'list'
as_tbl_graph(x, directed = TRUE, node_key = "name", ...)

## S3 method for class 'matrix'
as_tbl_graph(x, directed = TRUE, ...)

## S3 method for class 'network'
as_tbl_graph(x, ...)

## S3 method for class 'phylo'
as_tbl_graph(x, directed = NULL, ...)

## S3 method for class 'evonet'
as_tbl_graph(x, directed = TRUE, ...)

tbl_graph(nodes = NULL, edges = NULL, directed = TRUE, node_key = "name")

as_tbl_graph(x, ...)

## Default S3 method:
as_tbl_graph(x, ...)

is.tbl_graph(x)

Arguments

x	An object convertible to a tbl_graph
directed	Should the constructed graph be directed (defaults to TRUE)
...	Arguments passed on to the conversion function
mode	In case directed = TRUE should the edge direction be away from node or towards. Possible values are "out" (default) or "in".
node_key	The name of the column in nodes that character represented to and from columns should be matched against. If NA the first column is always chosen. This setting has no effect if to and from are given as integers.
nodes	A data.frame containing information about the nodes in the graph. If edges$to and/or edges$from are characters then they will be matched to the column named according to node_key in nodes, if it exists. If not, they will be matched to the first column.
edges	A data.frame containing information about the edges in the graph. The terminal nodes of each edge must either be encoded in a to and from column, or in the two first columns, as integers. These integers refer to nodes index.

Details

Constructors are provided for most data structures that resembles networks. If a class provides an igraph::as.igraph() method it is automatically supported.

Value

A tbl_graph object

Functions

• as_tbl_graph(data.frame): Method for edge table and set membership table

• as_tbl_graph(Node): Method to deal with Node objects from the data.tree package

• as_tbl_graph(dendrogram): Method for dendrogram objects

• as_tbl_graph(graphNEL): Method for handling graphNEL objects from the graph package (on Bioconductor)

• as_tbl_graph(graphAM): Method for handling graphAM objects from the graph package (on Bioconductor)

• as_tbl_graph(graphBAM): Method for handling graphBAM objects from the graph package (on Bioconductor)

• as_tbl_graph(hclust): Method for hclust objects

• as_tbl_graph(igraph): Method for igraph object. Simply subclasses the object into a tbl_graph

• as_tbl_graph(list): Method for adjacency lists and lists of node and edge tables

• as_tbl_graph(matrix): Method for edgelist, adjacency and incidence matrices

• as_tbl_graph(network): Method to handle network objects from the network package. Requires this packages to work.

• as_tbl_graph(phylo): Method for handling phylo objects from the ape package

• as_tbl_graph(evonet): Method for handling evonet objects from the ape package

• as_tbl_graph(default): Default method. tries to call igraph::as.igraph() on the input.

Examples

rstat_nodes <- data.frame(name = c("Hadley", "David", "Romain", "Julia"))
rstat_edges <- data.frame(from = c(1, 1, 1, 2, 3, 3, 4, 4, 4),
                            to = c(2, 3, 4, 1, 1, 2, 1, 2, 3))
tbl_graph(nodes = rstat_nodes, edges = rstat_edges)

tidygraph documentation built on June 22, 2024, 11:32 a.m.