Description Usage Arguments Details Value Note Author(s) See Also Examples

For our purposes an *edge matrix* is a matrix with two rows and as
many columns as there are edges. The entries in the first row are the
index of the node the edge is *from*, those in the second row indicate
the node the edge is *to*.

If the graph is “undirected” then the `duplicates`

option
can be used to indicate whether reciprocal edges are wanted. The
default is to leave them out. In this case the notions of *from*
and *to* are not relevant.

1 2 3 4 | ```
edgeMatrix(object, duplicates=FALSE)
eWV(g, eM, sep = ifelse(edgemode(g) == "directed", "->",
"--"), useNNames=FALSE)
pathWeights(g, p, eM=NULL)
``` |

`object` |
An object that inherits from |

`g` |
An object that inherits from |

`duplicates` |
Whether or not duplicate edges should be produced for “undirected” graphs. |

`eM` |
An edge matrix |

`sep` |
a character string to concatenate node labels in the edge label |

`useNNames` |
a logical; if TRUE, node names are used in the edge label; if FALSE, node indices are used |

`p` |
a vector of node names constituting a path in graph |

Implementations for `graphNEL`

, `clusterGraph`

and
`distGraph`

are available.

`edgeMatrix`

returns a matrix with two rows, *from* and *to*, and as many columns
as there are edges. Entries indicate the index in the node vector that
corresponds to the appropriate end of the edge.

`eWV`

uses the edge matrix to create an annotated vector of
edge weights.

`pathWeights`

returns an annotated vector of edge weights
for a specified path in a graph.

A path through an undirected graph may have several representations as a named vector of edges. Thus in the example, when the weights for path b-a-i are requested, the result is the pair of weights for edges a–b and a–i, as these are the edge labels computed for graph g1.

R. Gentleman

1 2 3 4 5 6 7 8 | ```
set.seed(123)
g1 <- randomGraph(letters[1:10], 1:4, p=.3)
edgeMatrix(g1)
g2 <- new("clusterGraph", clusters=list(a=c(1,2,3), b=c(4,5,6)))
em2 <- edgeMatrix(g2)
eWV(g1, edgeMatrix(g1))
eWV(g1, edgeMatrix(g1), useNNames=TRUE)
pathWeights(g1, c("b", "a", "i"))
``` |

```
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
from 1 1 1 1 1 1 1 2 2 2 2 2 3 4
to 7 9 2 4 5 6 8 6 10 4 5 8 8 5
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
from 4 4 5 5 6 6 7
to 6 8 6 8 10 8 9
1--7 1--9 1--2 1--4 1--5 1--6 1--8 2--6 2--10 2--4 2--5 2--8 3--8
1 1 1 1 1 1 1 2 1 1 1 1 1
4--5 4--6 4--8 5--6 5--8 6--10 6--8 7--9
1 1 1 1 1 1 1 1
a--g a--i a--b a--d a--e a--f a--h b--f b--j b--d b--e b--h c--h d--e d--f d--h
1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1
e--f e--h f--j f--h g--i
1 1 1 1 1
a--i a--b
1 1
```

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