How igraph functions handle attributes when the graph changes
Source:R/attributes.R
igraph-attribute-combination.Rd
Many times, when the structure of a graph is modified, vertices/edges map of
the original graph map to vertices/edges in the newly created (modified)
graph. For example simplify()
maps multiple edges to single
edges. igraph provides a flexible mechanism to specify what to do with the
vertex/edge attributes in these cases.
Details
The functions that support the combination of attributes have one or two
extra arguments called vertex.attr.comb
and/or edge.attr.comb
that specify how to perform the mapping of the attributes. E.g.
contract()
contracts many vertices into a single one, the
attributes of the vertices can be combined and stores as the vertex
attributes of the new graph.
The specification of the combination of (vertex or edge) attributes can be given as
a character scalar,
a function object or
a list of character scalars and/or function objects.
If it is a character scalar, then it refers to one of the predefined combinations, see their list below.
If it is a function, then the given function is expected to perform the combination. It will be called once for each new vertex/edge in the graph, with a single argument: the attribute values of the vertices that map to that single vertex.
The third option, a list can be used to specify different combination methods for different attributes. A named entry of the list corresponds to the attribute with the same name. An unnamed entry (i.e. if the name is the empty string) of the list specifies the default combination method. I.e.
list(weight="sum", "ignore")
specifies that the weight of the new edge should be sum of the weights of the corresponding edges in the old graph; and that the rest of the attributes should be ignored (=dropped).
Predefined combination functions
The following combination behaviors are predefined:
- "ignore"
The attribute is ignored and dropped.
- "sum"
The sum of the attributes is calculated. This does not work for character attributes and works for complex attributes only if they have a
sum
generic defined. (E.g. it works for sparse matrices from theMatrix
package, because they have asum
method.)- "prod"
The product of the attributes is calculated. This does not work for character attributes and works for complex attributes only if they have a
prod
function defined.- "min"
The minimum of the attributes is calculated and returned. For character and complex attributes the standard R
min
function is used.- "max"
The maximum of the attributes is calculated and returned. For character and complex attributes the standard R
max
function is used.- "random"
Chooses one of the supplied attribute values, uniformly randomly. For character and complex attributes this is implemented by calling
sample
.- "first"
Always chooses the first attribute value. It is implemented by calling the
head
function.- "last"
Always chooses the last attribute value. It is implemented by calling the
tail
function.- "mean"
The mean of the attributes is calculated and returned. For character and complex attributes this simply calls the
mean
function.- "median"
The median of the attributes is selected. Calls the R
median
function for all attribute types.- "concat"
Concatenate the attributes, using the
c
function. This results almost always a complex attribute.
See also
graph_attr()
, vertex_attr()
,
edge_attr()
on how to use graph/vertex/edge attributes in
general. igraph_options()
on igraph parameters.
Vertex, edge and graph attributes
delete_edge_attr()
,
delete_graph_attr()
,
delete_vertex_attr()
,
edge_attr()
,
edge_attr<-()
,
edge_attr_names()
,
graph_attr()
,
graph_attr<-()
,
graph_attr_names()
,
igraph-dollar
,
igraph-vs-attributes
,
set_edge_attr()
,
set_graph_attr()
,
set_vertex_attr()
,
vertex_attr()
,
vertex_attr<-()
,
vertex_attr_names()
Author
Gabor Csardi csardi.gabor@gmail.com
Examples
g <- make_graph(c(1, 2, 1, 2, 1, 2, 2, 3, 3, 4))
E(g)$weight <- 1:5
## print attribute values with the graph
igraph_options(print.graph.attributes = TRUE)
igraph_options(print.vertex.attributes = TRUE)
igraph_options(print.edge.attributes = TRUE)
## new attribute is the sum of the old ones
simplify(g, edge.attr.comb = "sum")
#> IGRAPH 3efa6c2 D-W- 4 3 --
#> + attr: weight (e/n)
#> + edges from 3efa6c2:
#> [1] 1->2 2->3 3->4
## collect attributes into a string
simplify(g, edge.attr.comb = toString)
#> IGRAPH ffc7fb6 D-W- 4 3 --
#> + attr: weight (e/c)
#> + edges from ffc7fb6:
#> [1] 1->2 2->3 3->4
## concatenate them into a vector, this creates a complex
## attribute
simplify(g, edge.attr.comb = "concat")
#> IGRAPH 94604d6 D-W- 4 3 --
#> + attr: weight (e/x)
#> + edges from 94604d6:
#> [1] 1->2 2->3 3->4
E(g)$name <- letters[seq_len(ecount(g))]
## both attributes are collected into strings
simplify(g, edge.attr.comb = toString)
#> IGRAPH 7fd1702 D-W- 4 3 --
#> + attr: weight (e/c), name (e/c)
#> + edges from 7fd1702:
#> [1] 1->2 2->3 3->4
## harmonic average of weights, names are dropped
simplify(g, edge.attr.comb = list(
weight = function(x) length(x) / sum(1 / x),
name = "ignore"
))
#> IGRAPH 4f32bcb D-W- 4 3 --
#> + attr: weight (e/n)
#> + edges from 4f32bcb:
#> [1] 1->2 2->3 3->4