test: merged and refactored conversion.R tests

R/conversion.R

@@ -649,7 +649,7 @@ as_adj_edge_list <- function(graph,
 graph_from_graphnel <- function(graphNEL, name = TRUE, weight = TRUE,
                                 unlist.attrs = TRUE) {
   if (!inherits(graphNEL, "graphNEL")) {
-    stop("Not a graphNEL graph")
+    cli::cli_abort("{.arg graphNEL} is {.obj_type_friendly {graphNEL}} and not a graphNEL graph")
   }
 
   al <- lapply(graph::edgeL(graphNEL), "[[", "edges")
@@ -740,7 +740,7 @@ as_graphnel <- function(graph) {
   ensure_igraph(graph)
 
   if (any_multiple(graph)) {
-    stop("multiple edges are not supported in graphNEL graphs")
+    cli::cli_abort("multiple edges are not supported in graphNEL graphs")
   }
 
   if ("name" %in% vertex_attr_names(graph) &&
@@ -1218,3 +1218,294 @@ as.undirected <- function(graph,
   lifecycle::deprecate_soft("2.1.0", "as.undirected()", "as_undirected()")
   as_undirected(graph = graph, mode = mode, edge.attr.comb = edge.attr.comb)
 }
+
+#' Create a graph from an edge list matrix
+#'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' `graph.edgelist()` was renamed to `graph_from_edgelist()` to create a more
+#' consistent API.
+#' @inheritParams graph_from_edgelist
+#' @keywords internal
+#' @export
+graph.edgelist <- function(el, directed = TRUE) { # nocov start
+  lifecycle::deprecate_soft("2.0.0", "graph.edgelist()", "graph_from_edgelist()")
+  graph_from_edgelist(el = el, directed = directed)
+} # nocov end
+
+#' Creating igraph graphs from data frames or vice-versa
+#'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' `graph.data.frame()` was renamed to `graph_from_data_frame()` to create a more
+#' consistent API.
+#' @inheritParams graph_from_data_frame
+#' @keywords internal
+#' @export
+graph.data.frame <- function(d, directed = TRUE, vertices = NULL) { # nocov start
+  lifecycle::deprecate_soft("2.0.0", "graph.data.frame()", "graph_from_data_frame()")
+  graph_from_data_frame(d = d, directed = directed, vertices = vertices)
+} # nocov end
+
+## ----------------------------------------------------------------
+##
+##   IGraph R package
+##   Copyright (C) 2005-2014  Gabor Csardi <[email protected]>
+##   334 Harvard street, Cambridge, MA 02139 USA
+##
+##   This program is free software; you can redistribute it and/or modify
+##   it under the terms of the GNU General Public License as published by
+##   the Free Software Foundation; either version 2 of the License, or
+##   (at your option) any later version.
+##
+##   This program is distributed in the hope that it will be useful,
+##   but WITHOUT ANY WARRANTY; without even the implied warranty of
+##   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##   GNU General Public License for more details.
+##
+##   You should have received a copy of the GNU General Public License
+##   along with this program; if not, write to the Free Software
+##   Foundation, Inc.,  51 Franklin Street, Fifth Floor, Boston, MA
+##   02110-1301 USA
+##
+## -----------------------------------------------------------------
+
+#' Creating igraph graphs from data frames or vice-versa
+#'
+#' This function creates an igraph graph from one or two data frames containing
+#' the (symbolic) edge list and edge/vertex attributes.
+#'
+#' `graph_from_data_frame()` creates igraph graphs from one or two data frames.
+#' It has two modes of operation, depending whether the `vertices`
+#' argument is `NULL` or not.
+#'
+#' If `vertices` is `NULL`, then the first two columns of `d`
+#' are used as a symbolic edge list and additional columns as edge attributes.
+#' The names of the attributes are taken from the names of the columns.
+#'
+#' If `vertices` is not `NULL`, then it must be a data frame giving
+#' vertex metadata. The first column of `vertices` is assumed to contain
+#' symbolic vertex names, this will be added to the graphs as the
+#' \sQuote{`name`} vertex attribute. Other columns will be added as
+#' additional vertex attributes. If `vertices` is not `NULL` then the
+#' symbolic edge list given in `d` is checked to contain only vertex names
+#' listed in `vertices`.
+#'
+#' Typically, the data frames are exported from some spreadsheet software like
+#' Excel and are imported into R via [read.table()],
+#' [read.delim()] or [read.csv()].
+#'
+#' All edges in the data frame are included in the graph, which may include
+#' multiple parallel edges and loops.
+#'
+#' `as_data_frame()` converts the igraph graph into one or more data
+#' frames, depending on the `what` argument.
+#'
+#' If the `what` argument is `edges` (the default), then the edges of
+#' the graph and also the edge attributes are returned. The edges will be in
+#' the first two columns, named `from` and `to`. (This also denotes
+#' edge direction for directed graphs.)  For named graphs, the vertex names
+#' will be included in these columns, for other graphs, the numeric vertex ids.
+#' The edge attributes will be in the other columns. It is not a good idea to
+#' have an edge attribute named `from` or `to`, because then the
+#' column named in the data frame will not be unique. The edges are listed in
+#' the order of their numeric ids.
+#'
+#' If the `what` argument is `vertices`, then vertex attributes are
+#' returned. Vertices are listed in the order of their numeric vertex ids.
+#'
+#' If the `what` argument is `both`, then both vertex and edge data
+#' is returned, in a list with named entries `vertices` and `edges`.
+#'
+#' @param d A data frame containing a symbolic edge list in the first two
+#'   columns. Additional columns are considered as edge attributes.  Since
+#'   version 0.7 this argument is coerced to a data frame with
+#'   `as.data.frame`.
+#' @param directed Logical scalar, whether or not to create a directed graph.
+#' @param vertices A data frame with vertex metadata, or `NULL`. See
+#'   details below. Since version 0.7 this argument is coerced to a data frame
+#'   with `as.data.frame`, if not `NULL`.
+#' @return An igraph graph object for `graph_from_data_frame()`, and either a
+#'   data frame or a list of two data frames named `edges` and
+#'   `vertices` for `as.data.frame`.
+#' @note For `graph_from_data_frame()` `NA` elements in the first two
+#' columns \sQuote{d} are replaced by the string \dQuote{NA} before creating
+#' the graph. This means that all `NA`s will correspond to a single
+#' vertex.
+#'
+#' `NA` elements in the first column of \sQuote{vertices} are also
+#' replaced by the string \dQuote{NA}, but the rest of \sQuote{vertices} is not
+#' touched. In other words, vertex names (=the first column) cannot be
+#' `NA`, but other vertex attributes can.
+#' @author Gabor Csardi \email{csardi.gabor@@gmail.com}
+#' @seealso [graph_from_literal()]
+#' for another way to create graphs, [read.table()] to read in tables
+#' from files.
+#' @keywords graphs
+#' @examples
+#'
+#' ## A simple example with a couple of actors
+#' ## The typical case is that these tables are read in from files....
+#' actors <- data.frame(
+#'   name = c(
+#'     "Alice", "Bob", "Cecil", "David",
+#'     "Esmeralda"
+#'   ),
+#'   age = c(48, 33, 45, 34, 21),
+#'   gender = c("F", "M", "F", "M", "F")
+#' )
+#' relations <- data.frame(
+#'   from = c(
+#'     "Bob", "Cecil", "Cecil", "David",
+#'     "David", "Esmeralda"
+#'   ),
+#'   to = c("Alice", "Bob", "Alice", "Alice", "Bob", "Alice"),
+#'   same.dept = c(FALSE, FALSE, TRUE, FALSE, FALSE, TRUE),
+#'   friendship = c(4, 5, 5, 2, 1, 1), advice = c(4, 5, 5, 4, 2, 3)
+#' )
+#' g <- graph_from_data_frame(relations, directed = TRUE, vertices = actors)
+#' print(g, e = TRUE, v = TRUE)
+#'
+#' ## The opposite operation
+#' as_data_frame(g, what = "vertices")
+#' as_data_frame(g, what = "edges")
+#'
+#' @export
+graph_from_data_frame <- function(d, directed = TRUE, vertices = NULL) {
+  d <- as.data.frame(d)
+  if (!is.null(vertices)) {
+    vertices <- as.data.frame(vertices)
+  }
+
+  if (ncol(d) < 2) {
+    cli::cli_abort("{.arg d} should contain at least two columns")
+  }
+
+  ## Handle if some elements are 'NA'
+  if (any(is.na(d[, 1:2]))) {
+    cli::cli_warn("In {.code d}, {.code NA} elements were replaced with string {.str NA}.")
+    d[, 1:2][is.na(d[, 1:2])] <- "NA"
+  }
+  if (!is.null(vertices) && any(is.na(vertices[, 1]))) {
+    cli::cli_warn("In {.code vertices[,1]}, {.code NA} elements were replaced with string {.str NA}.")
+    vertices[, 1][is.na(vertices[, 1])] <- "NA"
+  }
+
+  names <- unique(c(as.character(d[, 1]), as.character(d[, 2])))
+  if (!is.null(vertices)) {
+    names2 <- names
+    vertices <- as.data.frame(vertices)
+    if (ncol(vertices) < 1) {
+      cli::cli_abort("{.arg vertices} contains no rows")
+    }
+    names <- as.character(vertices[, 1])
+    if (any(duplicated(names))) {
+      cli::cli_abort("{.arg vertices} contains duplicated vertex names")
+    }
+    if (any(!names2 %in% names)) {
+      cli::cli_abort("Some vertex names in {.arg d} are not listed in {.arg vertices}")
+    }
+  }
+
+  # create graph
+  g <- make_empty_graph(n = 0, directed = directed)
+
+  # vertex attributes
+  attrs <- list(name = names)
+  if (!is.null(vertices)) {
+    if (ncol(vertices) > 1) {
+      for (i in 2:ncol(vertices)) {
+        newval <- vertices[, i]
+        if (inherits(newval, "factor")) {
+          newval <- as.character(newval)
+        }
+        attrs[[names(vertices)[i]]] <- newval
+      }
+    }
+  }
+
+  # add vertices
+  g <- add_vertices(g, length(names), attr = attrs)
+
+  # create edge list
+  from <- as.character(d[, 1])
+  to <- as.character(d[, 2])
+  edges <- rbind(match(from, names), match(to, names))
+
+  # edge attributes
+  attrs <- list()
+  if (ncol(d) > 2) {
+    for (i in 3:ncol(d)) {
+      newval <- d[, i]
+      if (inherits(newval, "factor")) {
+        newval <- as.character(newval)
+      }
+      attrs[[names(d)[i]]] <- newval
+    }
+  }
+
+  # add the edges
+  g <- add_edges(g, edges, attr = attrs)
+  g
+}
+
+#' @rdname graph_from_data_frame
+#' @param ... Passed to `graph_from_data_frame()`.
+#' @export
+from_data_frame <- function(...) constructor_spec(graph_from_data_frame, ...)
+
+## -----------------------------------------------------------------
+
+#' Create a graph from an edge list matrix
+#'
+#' `graph_from_edgelist()` creates a graph from an edge list. Its argument
+#' is a two-column matrix, each row defines one edge. If it is
+#' a numeric matrix then its elements are interpreted as vertex ids. If
+#' it is a character matrix then it is interpreted as symbolic vertex
+#' names and a vertex id will be assigned to each name, and also a
+#' `name` vertex attribute will be added.
+#'
+#' @concept Edge list
+#' @param el The edge list, a two column matrix, character or numeric.
+#' @param directed Whether to create a directed graph.
+#' @return An igraph graph.
+#'
+#' @family deterministic constructors
+#' @export
+#' @examples
+#' el <- matrix(c("foo", "bar", "bar", "foobar"), nc = 2, byrow = TRUE)
+#' graph_from_edgelist(el)
+#'
+#' # Create a ring by hand
+#' graph_from_edgelist(cbind(1:10, c(2:10, 1)))
+graph_from_edgelist <- function(el, directed = TRUE) {
+  if (!is.matrix(el) || ncol(el) != 2) {
+    cli::cli_abort("graph_from_edgelist expects a matrix with two columns")
+  }
+
+  if (nrow(el) == 0) {
+    res <- make_empty_graph(directed = directed)
+  } else {
+    if (is.character(el)) {
+      ## symbolic edge list
+      names <- unique(as.character(t(el)))
+      ids <- seq(names)
+      names(ids) <- names
+      res <- make_graph(unname(ids[t(el)]), directed = directed)
+      rm(ids)
+      V(res)$name <- names
+    } else {
+      ## normal edge list
+      res <- make_graph(t(el), directed = directed)
+    }
+  }
+
+  res
+}
+
+#' @rdname graph_from_edgelist
+#' @param ... Passed to `graph_from_edgelist()`.
+#' @export
+from_edgelist <- function(...) constructor_spec(graph_from_edgelist, ...)