## File: tbl_graph.Rd

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r-cran-tidygraph 1.2.0-1
 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144 % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data_frame.R, R/data_tree.R, R/dendrogram.R, % R/graph.R, R/hclust.R, R/igraph.R, R/list.R, R/matrix.R, R/network.R, % R/phylo.R, R/tbl_graph.R \name{as_tbl_graph.data.frame} \alias{as_tbl_graph.data.frame} \alias{as_tbl_graph.Node} \alias{as_tbl_graph.dendrogram} \alias{as_tbl_graph.graphNEL} \alias{as_tbl_graph.graphAM} \alias{as_tbl_graph.graphBAM} \alias{as_tbl_graph.hclust} \alias{as_tbl_graph.igraph} \alias{as_tbl_graph.list} \alias{as_tbl_graph.matrix} \alias{as_tbl_graph.network} \alias{as_tbl_graph.phylo} \alias{as_tbl_graph.evonet} \alias{tbl_graph} \alias{as_tbl_graph} \alias{as_tbl_graph.default} \alias{is.tbl_graph} \title{A data structure for tidy graph manipulation} \usage{ \method{as_tbl_graph}{data.frame}(x, directed = TRUE, ...) \method{as_tbl_graph}{Node}(x, directed = TRUE, mode = "out", ...) \method{as_tbl_graph}{dendrogram}(x, directed = TRUE, mode = "out", ...) \method{as_tbl_graph}{graphNEL}(x, ...) \method{as_tbl_graph}{graphAM}(x, ...) \method{as_tbl_graph}{graphBAM}(x, ...) \method{as_tbl_graph}{hclust}(x, directed = TRUE, mode = "out", ...) \method{as_tbl_graph}{igraph}(x, ...) \method{as_tbl_graph}{list}(x, directed = TRUE, node_key = "name", ...) \method{as_tbl_graph}{matrix}(x, directed = TRUE, ...) \method{as_tbl_graph}{network}(x, ...) \method{as_tbl_graph}{phylo}(x, directed = NULL, ...) \method{as_tbl_graph}{evonet}(x, directed = TRUE, ...) tbl_graph(nodes = NULL, edges = NULL, directed = TRUE, node_key = "name") as_tbl_graph(x, ...) \method{as_tbl_graph}{default}(x, ...) is.tbl_graph(x) } \arguments{ \item{x}{An object convertible to a \code{tbl_graph}} \item{directed}{Should the constructed graph be directed (defaults to \code{TRUE})} \item{...}{Arguments passed on to the conversion function} \item{mode}{In case \code{directed = TRUE} should the edge direction be away from node or towards. Possible values are \code{"out"} (default) or \code{"in"}.} \item{node_key}{The name of the column in \code{nodes} that character represented \code{to} and \code{from} columns should be matched against. If \code{NA} the first column is always chosen. This setting has no effect if \code{to} and \code{from} are given as integers.} \item{nodes}{A \code{data.frame} containing information about the nodes in the graph. If \code{edges$to} and/or \code{edges$from} are characters then they will be matched to the column named according to \code{node_key} in nodes, if it exists. If not, they will be matched to the first column.} \item{edges}{A \code{data.frame} containing information about the edges in the graph. The terminal nodes of each edge must either be encoded in a \code{to} and \code{from} column, or in the two first columns, as integers. These integers refer to \code{nodes} index.} } \value{ A \code{tbl_graph} object } \description{ The \code{tbl_graph} class is a thin wrapper around an \code{igraph} object that provides methods for manipulating the graph using the tidy API. As it is just a subclass of \code{igraph} every igraph method will work as expected. A \code{grouped_tbl_graph} is the equivalent of a \code{grouped_df} where either the nodes or the edges has been grouped. The \code{grouped_tbl_graph} is not constructed directly but by using the \code{\link[=group_by]{group_by()}} verb. After creation of a \code{tbl_graph} the nodes are activated by default. The context can be changed using the \code{\link[=activate]{activate()}} verb and affects all subsequent operations. Changing context automatically drops any grouping. The current active context can always be extracted with \code{\link[=as_tibble]{as_tibble()}}, which drops the graph structure and just returns a \code{tbl_df} or a \code{grouped_df} depending on the state of the \code{tbl_graph}. The returned context can be overriden by using the \code{active} argument in \code{\link[=as_tibble]{as_tibble()}}. } \details{ Constructors are provided for most data structures that resembles networks. If a class provides an \code{\link[igraph:as.igraph]{igraph::as.igraph()}} method it is automatically supported. } \section{Methods (by generic)}{ \itemize{ \item \code{as_tbl_graph}: Method for edge table and set membership table \item \code{as_tbl_graph}: Method to deal with Node objects from the data.tree package \item \code{as_tbl_graph}: Method for dendrogram objects \item \code{as_tbl_graph}: Method for handling graphNEL objects from the graph package (on Bioconductor) \item \code{as_tbl_graph}: Method for handling graphAM objects from the graph package (on Bioconductor) \item \code{as_tbl_graph}: Method for handling graphBAM objects from the graph package (on Bioconductor) \item \code{as_tbl_graph}: Method for hclust objects \item \code{as_tbl_graph}: Method for igraph object. Simply subclasses the object into a \code{tbl_graph} \item \code{as_tbl_graph}: Method for adjacency lists and lists of node and edge tables \item \code{as_tbl_graph}: Method for edgelist, adjacency and incidence matrices \item \code{as_tbl_graph}: Method to handle network objects from the \code{network} package. Requires this packages to work. \item \code{as_tbl_graph}: Method for handling phylo objects from the ape package \item \code{as_tbl_graph}: Method for handling evonet objects from the ape package \item \code{as_tbl_graph}: Default method. tries to call \code{\link[igraph:as.igraph]{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) }