Access and Modify a Cograph Network

These functions read and replace the parts of a cograph_network object created by as_cograph. The getters return the node table, the edge table, the node labels, the node groups, the source type, the stored estimation data, the metadata list, and the counts of nodes and edges. The setters return a modified copy of the network.

Usage

get_nodes(x)

get_edges(x)

get_labels(x)

get_source(x)

get_data(x)

get_meta(x)

set_nodes(x, nodes_df)

set_edges(x, edges_df)

set_layout(x, layout_df)

set_groups(
  x,
  groups = NULL,
  type = c("group", "cluster", "layer"),
  nodes = NULL,
  layers = NULL,
  clusters = NULL
)

get_groups(x)

nodes(x)

is_directed(x)

n_nodes(x)

n_edges(x)

Arguments

x

A cograph_network object. is_directed() also accepts a CographNetwork or an igraph object.

nodes_df

A data frame of node information. A missing id column is filled with row numbers and a missing label column with the ids. The stored weight matrix is rebuilt from the new node table.

edges_df

A data frame with columns from and to (integer row numbers into the node table) and an optional weight column, which defaults to 1. Extra columns are kept. Each edge may appear once, and an undirected network counts A-B and B-A as the same edge.

layout_df

A data frame with x and y columns, or a matrix whose first two columns are used, with one row per node.

groups

Node groupings in one of these formats:

A character string naming a community detection method of detect_communities ("louvain", "walktrap", "fast_greedy", "label_prop", "infomap", "leiden"), which requires the igraph package.
A named list mapping each group name to a vector of node labels, for example list(A = c("N1", "N2"), B = c("N3", "N4")).
An unnamed vector with one group assignment per node, in node order.
A data frame with a node (or nodes) column and one of layer, cluster or group (plural forms are accepted and normalized to the singular).
NULL, in which case nodes and one of layers or clusters supply the grouping.

type

Group type stored by set_groups(). One of "group" (default), "cluster" or "layer". It is ignored when layers or clusters is given, since the type then follows from the argument used.

nodes

Character vector of node labels, used with layers or clusters to give groupings as vectors. When NULL, the assignments follow the node order of the network.

layers

Character or factor vector of layer assignments, the same length as nodes.

clusters

Character or factor vector of cluster assignments, the same length as nodes.

Value

get_nodes(), nodes(): The node table, with id and label columns plus layout coordinates or other metadata columns when present. nodes() is a deprecated alias of get_nodes() and signals a deprecation warning.
get_edges(): A data frame with one row per edge and columns from and to (integer row numbers into the node table), weight, and any extra edge columns. An undirected network stores one row per unordered pair. as.data.frame() returns the same table with node labels as endpoints.
get_labels(): A character vector of node labels.
get_groups(): A data frame with a node column and one of layer, cluster or group, or NULL when no groups are set.
get_source(): A character string naming the input type (for example "matrix", "tna", "igraph", "edgelist"), or "unknown".
get_data(): The original estimation data (for example the sequence data of a tna model), or NULL when none is stored.
get_meta(): A list with component source (input type). Networks built from a tna model also carry tna (type, group name and group index).
n_nodes(), n_edges(): An integer count. Each undirected edge counts once.
is_directed(): A single logical value.
set_nodes(), set_edges(), set_layout(), set_groups(): The modified cograph_network. set_layout() writes the coordinates into the x and y columns of the node table. set_groups() stores the grouping as node_groups for use by the group-aware plot functions. It stops with an error when a node is assigned twice, when a node is missing from the assignment or unknown to the network, and when fewer than two groups result. set_edges() raises an error of class cograph_bad_selection for endpoints outside the node table and for duplicated edges.

Examples

net <- as_cograph(regulation_net)
get_edges(net)
#>    from to weight
#> 1     4  1   0.28
#> 2     5  1   0.05
#> 3     6  1   0.30
#> 4     9  1   0.14
#> 5     7  2   0.11
#> 6    10  2   0.21
#> 7     2  3   0.13
#> 8     5  3   0.15
#> 9     7  3   0.07
#> 10    8  3   0.33
#> 11    9  3   0.17
#> 12   10  3   0.49
#> 13    3  4   0.16
#> 14    8  4   0.43
#> 15   10  4   0.39
#> 16    1  5   0.35
#> 17    6  5   0.35
#> 18    7  5   0.42
#> 19    8  5   0.07
#> 20    2  6   0.40
#> 21    4  6   0.34
#> 22    4  7   0.17
#> 23    2  8   0.49
#> 24    9  8   0.39
#> 25    2  9   0.20
#> 26    3  9   0.37
#> 27    6  9   0.14
#> 28    1 10   0.27
#> 29    2 10   0.36
#> 30    9 10   0.23

Usage

Arguments

Value

See also

Examples