[ subsets a GraphSpace object along two independent
dimensions: the first index (i) selects nodes; the second (j)
selects edges.
[[ retrieves a single named slot from a
GraphSpace object.
Usage
# S4 method for class 'GraphSpace,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]
# S4 method for class 'GraphSpace'
x[[i, j, ...]]Arguments
- x
A
GraphSpaceobject.- i
A node selection. Accepted forms:
A character vector of node names.
An integer vector of positional indices into
@nodes.A logical vector whose length matches the number of nodes.
If omitted, all nodes are retained.
- j
An edge selection. Accepted forms:
An integer vector of positional indices into
@edges.A logical vector whose length matches the number of edges.
Because
[evaluates its arguments in the calling environment before dispatch, unquoted column names such asname1 == "n1"cannot be used directly. Pre-evaluate the expression against the edge table first (e.g.gs_edges(gs)$name1 == "n1"), or usegs_subset_edgeswhich supports unquoted predicates via data masking. If omitted, all edges are retained (subject to node-filter cascade).- ...
Currently unused.
- drop
Ignored; accepted for S4 method compatibility only.
Details
Mental model: unlike a data frame, where [i, j] means rows
and columns of the same table, for GraphSpace the two indices
address the two primary components of the graph: nodes (i) and
edges (j). Neither index subsets columns, they select graph
entities.
Synchronization rules:
x[i, ]— node-induced subgraph. After selecting nodes, edges are automatically pruned to those whose both endpoints survived. Normalized coordinates are preserved.x[, j]— edge selection. The node set is not modified; no node pruning occurs.x[i, j]— combined selection. Node filtering is applied first. Edge indexjis resolved against the original edge table; an edge survives only if it appears injand both its endpoints survived node filtering (silent intersection).
Note for [[: the slot accessor is read-only. Use the
dedicated replacement methods (gs_image<-,
gs_fdata<-, gs_vertex_attr<-, etc.) to
modify slot contents.
Examples
library(RGraphSpace)
library(igraph)
g <- make_star(10, mode = "out")
V(g)$nodeSize <- runif(vcount(g), 1, 10)
E(g)$weight <- runif(ecount(g), 0, 1)
gs <- GraphSpace(g)
#> Validating the 'igraph' object...
#> Vertex attributes 'x' and 'y' missing; computing layout...
#> Vertex attribute 'name' missing; assigning names...
#> Ignoring graph-level attributes: 'name', 'mode', 'center'
#> Creating a 'GraphSpace' object...
gs <- normalizeGraphSpace(gs)
#> Normalizing node coordinates to graph space...
#--- [ examples ---
# Node-induced subgraph: keep named nodes, prune dangling edges
gs[c("n1", "n2", "n3"), ]
#> A GraphSpace-class object for:
#> IGRAPH 0738946 DNW- 3 2 --
#> + attr: x (v/n), y (v/n), name (v/c), nodeLabel (v/c), nodeSize (v/n),
#> | arrowType (e/n), weight (e/n)
#> + node spatial boundaries: normalized to graph space
#> | x: [0, 2] -> [0, 1] (cols)
#> | y: [-2, 0] -> [0, 1] (rows)
# Node-induced subgraph by integer position
gs[1:4, ]
#> A GraphSpace-class object for:
#> IGRAPH ddd73d7 DNW- 4 3 --
#> + attr: x (v/n), y (v/n), name (v/c), nodeLabel (v/c), nodeSize (v/n),
#> | arrowType (e/n), weight (e/n)
#> + node spatial boundaries: normalized to graph space
#> | x: [0, 2] -> [0, 1] (cols)
#> | y: [-2, 1] -> [0, 1] (rows)
# Node-induced subgraph by pre-evaluated logical mask
gs[gs$nodeSize > 5, ]
#> A GraphSpace-class object for:
#> IGRAPH 3905eb4 DNW- 5 4 --
#> + attr: x (v/n), y (v/n), name (v/c), nodeLabel (v/c), nodeSize (v/n),
#> | arrowType (e/n), weight (e/n)
#> + node spatial boundaries: normalized to graph space
#> | x: [-2, 2] -> [0, 1] (cols)
#> | y: [-3, 3] -> [0, 1] (rows)
# Edge selection only: keep all nodes
gs[, 1:3]
#> A GraphSpace-class object for:
#> IGRAPH f18440b DNW- 10 3 --
#> + attr: x (v/n), y (v/n), name (v/c), nodeLabel (v/c), nodeSize (v/n),
#> | arrowType (e/n), weight (e/n)
#> + node spatial boundaries: normalized to graph space
#> | x: [-4, 4] -> [0, 1] (cols)
#> | y: [-3, 3] -> [0, 1] (rows)
gs[, gs_edges(gs)$weight > 0.5]
#> A GraphSpace-class object for:
#> IGRAPH b9c4752 DNW- 10 4 --
#> + attr: x (v/n), y (v/n), name (v/c), nodeLabel (v/c), nodeSize (v/n),
#> | arrowType (e/n), weight (e/n)
#> + node spatial boundaries: normalized to graph space
#> | x: [-4, 4] -> [0, 1] (cols)
#> | y: [-3, 3] -> [0, 1] (rows)
# Edge selection by endpoint: 'name1' and 'name2' must be pre-evaluated
# when using [, because [ evaluates j in the calling environment.
# Use gs_subset_edges() for unquoted predicate expressions instead.
gs[, gs_edges(gs)$name1 == "n1"]
#> A GraphSpace-class object for:
#> IGRAPH 8a9443b DNW- 10 9 --
#> + attr: x (v/n), y (v/n), name (v/c), nodeLabel (v/c), nodeSize (v/n),
#> | arrowType (e/n), weight (e/n)
#> + node spatial boundaries: normalized to graph space
#> | x: [-4, 4] -> [0, 1] (cols)
#> | y: [-3, 3] -> [0, 1] (rows)
gs[, gs_edges(gs)$name1 == "n1" & gs_edges(gs)$name2 == "n2"]
#> A GraphSpace-class object for:
#> IGRAPH 488131b DNW- 10 1 --
#> + attr: x (v/n), y (v/n), name (v/c), nodeLabel (v/c), nodeSize (v/n),
#> | arrowType (e/n), weight (e/n)
#> + node spatial boundaries: normalized to graph space
#> | x: [-4, 4] -> [0, 1] (cols)
#> | y: [-3, 3] -> [0, 1] (rows)
gs[, quote(name1 == "n1" & name2 == "n2")]
#> A GraphSpace-class object for:
#> IGRAPH 169365c DNW- 10 1 --
#> + attr: x (v/n), y (v/n), name (v/c), nodeLabel (v/c), nodeSize (v/n),
#> | arrowType (e/n), weight (e/n)
#> + node spatial boundaries: normalized to graph space
#> | x: [-4, 4] -> [0, 1] (cols)
#> | y: [-3, 3] -> [0, 1] (rows)
# Combined: node filter first, then edge intersection
gs[c("n1", "n2", "n3"), gs_edges(gs)$weight > 0.5]
#> A GraphSpace-class object for:
#> IGRAPH ec725c5 DNW- 3 1 --
#> + attr: x (v/n), y (v/n), name (v/c), nodeLabel (v/c), nodeSize (v/n),
#> | arrowType (e/n), weight (e/n)
#> + node spatial boundaries: normalized to graph space
#> | x: [0, 2] -> [0, 1] (cols)
#> | y: [-2, 0] -> [0, 1] (rows)
gs[c("n1", "n2", "n3"), gs_edges(gs)$name1 == "n1"]
#> A GraphSpace-class object for:
#> IGRAPH ca853b0 DNW- 3 2 --
#> + attr: x (v/n), y (v/n), name (v/c), nodeLabel (v/c), nodeSize (v/n),
#> | arrowType (e/n), weight (e/n)
#> + node spatial boundaries: normalized to graph space
#> | x: [0, 2] -> [0, 1] (cols)
#> | y: [-2, 0] -> [0, 1] (rows)
#--- [[ examples ---
gs[["nodes"]] # same as getGraphSpace(gs, "nodes")
#> vertex x y name nodeLabel nodeSize
#> n1 1 0.5451600 0.4787943 n1 n1 8.737057
#> n2 2 0.7721881 0.3047887 n2 n2 8.468647
#> n3 3 0.5774618 0.2561736 n3 n3 3.221987
#> n4 4 0.6793070 0.5686969 n4 n4 2.646892
#> n5 5 0.4153308 0.6557862 n5 n5 9.444512
#> n6 6 0.6049855 0.7863138 n6 n6 6.688782
#> n7 7 0.3541184 0.2136862 n7 n7 5.548468
#> n8 8 0.3919361 0.4423731 n8 n8 3.130393
#> n9 9 0.9000000 0.5565967 n9 n9 4.802347
#> n10 10 0.1000000 0.5790244 n10 n10 1.883933
gs[["edges"]] # same as getGraphSpace(gs, "edges")
#> vertex1 vertex2 name1 name2 arrowType weight curve_weight is_multiple
#> 1 1 2 n1 n2 1 0.3958730 1 FALSE
#> 2 1 3 n1 n3 1 0.5715212 1 FALSE
#> 3 1 4 n1 n4 1 0.8931345 1 FALSE
#> 4 1 5 n1 n5 1 0.6063836 1 FALSE
#> 5 1 6 n1 n6 1 0.3435077 1 FALSE
#> 6 1 7 n1 n7 1 0.3121115 1 FALSE
#> 7 1 8 n1 n8 1 0.9935579 1 FALSE
#> 8 1 9 n1 n9 1 0.2513228 1 FALSE
#> 9 1 10 n1 n10 1 0.1391213 1 FALSE
#> is_loop
#> 1 FALSE
#> 2 FALSE
#> 3 FALSE
#> 4 FALSE
#> 5 FALSE
#> 6 FALSE
#> 7 FALSE
#> 8 FALSE
#> 9 FALSE
gs[["graph"]] # same as getGraphSpace(gs, "graph")
#> IGRAPH 8a9443b DNW- 10 9 --
#> + attr: x (v/n), y (v/n), name (v/c), nodeLabel (v/c), nodeSize (v/n),
#> | arrowType (e/n), weight (e/n)
#> + edges from 8a9443b (vertex names):
#> [1] n1->n2 n1->n3 n1->n4 n1->n5 n1->n6 n1->n7 n1->n8 n1->n9 n1->n10
gs[["fdata"]] # same as getGraphSpace(gs, "fdata")
#> 0 x 0 Matrix of class "dgeMatrix"
#> <0 x 0 matrix>