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#' Create a graph object
#'
#' @description
#'
#' Generates a graph object with the option to use node data frames (ndfs)
#' and/or edge data frames (edfs) to populate the initial graph.
#'
#' @param nodes_df An optional data frame containing, at minimum, a column
#' (called `id`) which contains node IDs for the graph. Additional columns
#' (node attributes) can be included with values for the named node attribute.
#' @param edges_df An optional data frame containing, at minimum, two columns
#' (called `from` and `to`) where node IDs are provided. Additional columns
#' (edge attributes) can be included with values for the named edge attribute.
#' @param directed With `TRUE` (the default) or `FALSE`, either directed or
#' undirected edge operations will be generated, respectively.
#' @param graph_name An optional string for labeling the graph object.
#' @param attr_theme The theme (i.e., collection of `graph`, `node`, and `edge`
#' global graph attributes) to use for this graph. The default theme is called
#' `default`; there are hierarchical layout themes called `lr`, `tb`, `rl`,
#' and `bt` (these operate from left-to-right, top-to-bottom, right-to-left,
#' and bottom-to-top); and, for larger graphs, the `fdp` theme provides a
#' force directed layout. If this is set to `NULL` then no global graph
#' attributes will be applied to the graph upon creation.
#' @param write_backups An option to write incremental backups of changing graph
#' states to disk. If `TRUE`, a subdirectory within the working directory will
#' be created and used to store `RDS` files. The default value is `FALSE` so
#' one has to opt in to use this functionality.
#' @param display_msgs An option to display messages primarily concerned with
#' changes in graph selections. By default, this is `FALSE`.
#'
#' @return A graph object of class `dgr_graph`.
#'
#' @examples
#' # With `create_graph()` we can
#' # simply create an empty graph (and
#' # add in nodes and edges later
#' # with other functions)
#' graph <- create_graph()
#'
#' # A graph can be created with
#' # nodes and without having any edges;
#' # this can be done in 2 steps:
#' # 1. create a node data frame (ndf)
#' # using `create_node_df()`
#' ndf <-
#' create_node_df(n = 4)
#'
#' # 2. create a new graph object with
#' # `create_graph()` and then pass
#' # in the ndf to `nodes_df`
#' graph <-
#' create_graph(
#' nodes_df = ndf)
#'
#' # Get information on the graph's nodes
#' graph %>%
#' get_node_info()
#'
#' # You can create a similar graph with
#' # just nodes but also providing a
#' # range of attributes for the nodes
#' # (e.g., types, labels, or arbitrary
#' # 'values')
#' ndf <-
#' create_node_df(
#' n = 4,
#' label = TRUE,
#' type = c("type_1", "type_1",
#' "type_5", "type_2"),
#' shape = c("circle", "circle",
#' "rectangle", "rectangle"),
#' values = c(3.5, 2.6, 9.4, 2.7))
#'
#' graph <-
#' create_graph(nodes_df = ndf)
#'
#' # Get information on the graph's
#' # internal node data frame (ndf)
#' graph %>%
#' get_node_df()
#'
#' # A graph can also be created by
#' # specifying both the nodes and
#' # edges; create an edge data frame
#' # (edf) using the `create_edge_df()`
#' # function:
#' edf <-
#' create_edge_df(
#' from = c(1, 2, 3),
#' to = c(4, 3, 1),
#' rel = "leading_to",
#' values = c(7.3, 2.6, 8.3))
#'
#' # Create the graph object with
#' # `create_graph()` and pass in the
#' # ndf and edf objects
#' graph <-
#' create_graph(
#' nodes_df = ndf,
#' edges_df = edf)
#'
#' # Get information on the graph's
#' # internal edge data frame (edf)
#' graph %>% get_edge_df()
#'
#' # Get information on the graph's
#' # internal node data frame (ndf)
#' graph %>% get_node_df()
#'
#' @export
create_graph <- function(
nodes_df = NULL,
edges_df = NULL,
directed = TRUE,
graph_name = NULL,
attr_theme = "default",
write_backups = FALSE,
display_msgs = FALSE
) {
## DF: `graph_info`
# Get the time of graph creation
graph_time <- Sys.time()
# Get the locale's time zone
graph_tz <- Sys.timezone()
# Generate a random 8-character, alphanumeric
# string to use as a graph ID
graph_id <-
replicate(8, sample(c(LETTERS, letters, 0:9), 1)) %>%
paste(collapse = "")
# Create the `graph_info` data frame
graph_info <-
data.frame(
graph_id = as.character(graph_id),
graph_name = as.character(paste0("graph_", graph_id)),
graph_time = graph_time,
graph_tz = graph_tz,
write_backups = write_backups,
display_msgs = display_msgs,
stringsAsFactors = FALSE
)
# Insert a user-defined `graph_name` if supplied
if (!is.null(graph_name)) {
graph_info[1, 2] <- as.character(graph_name)
}
## DF: `global_attrs`
# Create an empty table for global graph attributes
global_attrs <-
data.frame(
attr = character(0L),
value = character(0L),
attr_type = character(0L),
stringsAsFactors = FALSE
)
# If `attr_theme` is `default` then populate the
# `global_attrs` data frame with global graph attrs
if (inherits(attr_theme, "character")) {
global_attrs <-
switch(
attr_theme,
default = attr_theme_default(),
lr = attr_theme_lr(),
tb = attr_theme_tb(),
rl = attr_theme_rl(),
bt = attr_theme_bt(),
fdp = attr_theme_fdp(),
kk = attr_theme_kk(),
cli::cli_abort(
"The value for `attr_theme` doesn't refer to any available theme."
)
)
} else if (is.null(attr_theme)) {
global_attrs <-
data.frame(
attr = character(0L),
value = character(0L),
attr_type = character(0L),
stringsAsFactors = FALSE)
}
## DF: `nodes_df`
# Create an empty node data frame (`ndf`)
ndf <-
data.frame(
id = integer(0L),
type = character(0L),
label = character(0L),
stringsAsFactors = FALSE
)
## DF: `edges_df`
# Create an empty edge data frame (`edf`)
edf <-
data.frame(
id = integer(0L),
from = integer(0L),
to = integer(0L),
rel = character(0L),
stringsAsFactors = FALSE
)
## DF: `node_selection`
# Create an empty node selection data frame (`nsdf`)
nsdf <-
data.frame(node = integer(0L), stringsAsFactors = FALSE)
## DF: `edge_selection`
# Create an empty edge selection data frame (`esdf`)
esdf <-
data.frame(
edge = integer(0L),
from = integer(0L),
to = integer(0L),
stringsAsFactors = FALSE
)
## DF: `graph_actions`
# Create an empty `graph_actions` data frame
graph_actions <-
data.frame(
action_index = integer(0L),
action_name = character(0L),
expression = character(0L),
stringsAsFactors = FALSE
)
## DF: `graph_log`
# Create an empty `graph_log` data frame
graph_log <-
data.frame(
version_id = integer(0L),
function_used = character(0L),
# Datetime of length 0
time_modified = structure(numeric(0L), class = c("POSIXct", "POSIXt")),
duration = numeric(0L),
nodes = integer(0L),
edges = integer(0L),
d_n = integer(0L),
d_e = integer(0L),
stringsAsFactors = FALSE
)
## list: `cache`
# Create an empty `cache` list object
cache <- list()
## Empty Graph
# Initialize a graph object
graph <-
list(
graph_info = graph_info,
nodes_df = ndf,
edges_df = edf,
global_attrs = global_attrs,
directed = directed, # TRUE or FALSE
last_node = 0,
last_edge = 0,
node_selection = nsdf,
edge_selection = esdf,
cache = cache,
graph_actions = graph_actions,
graph_log = graph_log
)
attr(graph, "class") <- "dgr_graph"
# If neither an ndf nor both ndf & edf provided,
# create an initialized graph with no nodes or edges
if (is.null(nodes_df) && is.null(edges_df)) {
# Get the name of the function
fcn_name <- get_calling_fcn()
# Update the `graph_log` df with an action
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = 1L,
function_used = fcn_name,
time_modified = graph_time,
duration = graph_function_duration(graph_time),
nodes = nrow(graph$nodes_df),
edges = nrow(graph$edges_df),
d_n = nrow(graph$nodes_df),
d_e = nrow(graph$edges_df)
)
} else if (!is.null(nodes_df) && is.null(edges_df)) {
# If only an ndf is provided, create a graph
# just containing nodes
# Transform any `tbl_df` object to a `data.frame`
if (inherits(nodes_df, "tbl_df")) {
nodes_df <- as.data.frame(nodes_df, stringsAsFactors = FALSE)
}
# Force the `type` and `label` columns
# to be of the character class
for (i in 2:3) {
nodes_df[, i] <- as.character(nodes_df[, i])
}
# Bind the nodes to the `nodes_df` df in the graph
graph$nodes_df <- dplyr::bind_rows(graph$nodes_df, nodes_df)
# Modify the `last_node` vector
graph$last_node <- nrow(nodes_df)
# Get the name of the function
fcn_name <- get_calling_fcn()
# Update the `graph_log` df with an action
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = 1L,
function_used = fcn_name,
time_modified = graph_time,
duration = graph_function_duration(graph_time),
nodes = nrow(graph$nodes_df),
edges = nrow(graph$edges_df),
d_n = nrow(graph$nodes_df),
d_e = nrow(graph$edges_df)
)
} else if (!is.null(nodes_df) && !is.null(edges_df)) {
# If an ndf and edf both provided, create a graph
# initially populated with both nodes and edges
# Transform any `tbl_df` object to a `data.frame`
if (inherits(nodes_df, "tbl_df")) {
nodes_df <- as.data.frame(nodes_df, stringsAsFactors = FALSE)
}
# Transform any `tbl_df` object to a `data.frame`
if (inherits(edges_df, "tbl_df")) {
edges_df <- as.data.frame(edges_df, stringsAsFactors = FALSE)
}
# Force the `type` and `label` columns
# to be of the character class
for (i in 2:3) {
nodes_df[, i] <- as.character(nodes_df[, i])
}
# Bind the nodes to the `nodes_df` df in the graph
graph$nodes_df <-
dplyr::bind_rows(graph$nodes_df, nodes_df)
# Modify the `last_node` vector
graph$last_node <- nrow(nodes_df)
# Ensure that the edf has the correct classes
if (inherits(edges_df, "data.frame") && ncol(edges_df) > 2) {
# Force the rel column to be of the character class
edges_df$rel <- as.character(edges_df$rel)
}
# Bind the edges to the `edges_df` df in the graph
graph$edges_df <-
dplyr::bind_rows(graph$edges_df, edges_df)
# Modify the `last_edge` vector
graph$last_edge <- nrow(edges_df)
# Get the name of the function
fcn_name <- get_calling_fcn()
# Update the `graph_log` df with an action
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = 1L,
function_used = fcn_name,
time_modified = graph_time,
duration = graph_function_duration(graph_time),
nodes = nrow(graph$nodes_df),
edges = nrow(graph$edges_df),
d_n = nrow(graph$nodes_df),
d_e = nrow(graph$edges_df))
}
# Add the `graph_log` df to the graph object
graph$graph_log <- graph_log
# Write graph backup if the option is set
if (graph$graph_info$write_backups) {
save_graph_as_rds(graph = graph)
}
# If neither an ndf nor both ndf & edf provided,
# return the initialized graph with no nodes or edges
graph
}
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