| write.graph {igraph} | R Documentation |
write.graph is a general function for exporting
graphs to foreign file formats, however not many formats are
implemented right now.
write.graph(graph, file, format=c("edgelist", "pajek", "ncol",
"lgl", "graphml", "dimacs", "gml", "dot", "leda"), ...)
graph |
The graph to export. |
file |
A connection or a string giving the file name to write the graph to. |
format |
Character string giving the file format. Right now
|
... |
Other, format specific arguments, see below. |
A NULL, invisibly.
The edgelist format is a simple text file, with one edge in a
line, the two vertex ids separated by a space character. The file is
sorted by the first and the second column. This format has no
additional arguments.
The Pajek format is a text file, see read.graph for
details. Appropriate vertex and edge attributes are also written to
the file. This format has no additional arguments.
From version 0.6.1 igraph handles bipartite graphs when writing to Pajek files. As Pajek is less flexible for bipartite graphs (the numeric ids of the vertices must be sorted according to vertex type), igraph might need to reorder the vertices when writing a bipartite Pajek file. This effectively means that numeric vertex ids usually change when a bipartite graph is written to a Pajek file, and then read back into igraph.
The GraphML format is a flexible XML based format. See
read.graph for GraphML details. Vertex and edge
attributes are also written to the file. Additional argument:
Logical scalar, whether you want to add a prefix
to the graph, vertex and edge attribute names, to ensure their
uniqueness. Defaults to TRUE.
The dot format is used by the popular GraphViz program. Vertex and edge attributes are written to the file. There are no additional arguments for this format.
The lgl format is also a simple text file, this is the
format expected by the 'Large Graph Layout' layout generator software.
See read.graph for details.
Additional arguments:
If you want to write symbolic vertex names instead of
vertex ids, supply the name of the vertex attribute containing the
symbolic names here. By default the ‘name’ attribute is
used if there is one. Supply NULL if you want to use numeric
vertex ids even if there is a ‘name’ vertex attribute.
If you want to write edge weights to the file, supply
the name of the edge attribute here. By defaults the vertex
attribute ‘weights’ are used if they are installed.
Supply NULL here if you want to omit the weights.
Logical, if TRUE the isolate vertices are
also written to the file, they are omitted by default.
The ncol format is also used by LGL, it is a text file, see
read.graph for details.
Additional arguments:
If you want to write symbolic vertex names instead of
vertex ids, supply the name of the vertex attribute containing the
symbolic names here. By default the ‘name’ attribute is
used if there is one. Supply NULL if you want to use numeric
vertex ids even if there is a ‘name’ vertex attribute.
If you want to write edge weights to the file, supply
the name of the edge attribute here. By defaults the vertex
attribute ‘weights’ are used if they are installed.
Supply NULL here if you want to omit the weights.
The dimacs file format, more specifically the
version for network flow problems, see the files at
ftp://dimacs.rutgers.edu/pub/netflow/general-info/
This is a line-oriented text file (ASCII) format. The first
character of each line defines the type of the line. If the first
character is c the line is a comment line and it is
ignored. There is one problem line (p in the file, it
must appear before any node and arc descriptor lines. The problem
line has three fields separated by spaces: the problem type
(min, max or asn), the
number of vertices and number of edges in the graph.
Exactly two node identification lines are expected
(n), one for the source, one for the target vertex.
These have two fields: the id of the vertex and the type of the
vertex, either s (=source) or t
(=target). Arc lines start with a and have three
fields: the source vertex, the target vertex and the edge capacity.
Vertex ids are numbered from 1.
Additional arguments:
The id of the source vertex, if NULL (the
default) then it is taken from the source graph attribute.
The id of the target vertex, if NULL (the
default) then it is taken from the target graph attribute.
A numeric vector giving the edge capacities. If
NULL (the default) then it is taken from the
capacity edge attribute.
GML is a quite general textual format, see http://www.infosun.fim.uni-passau.de/Graphlet/GML/ for details.
The graph, vertex and edges attributes are written to the file as well, if they are numeric of string.
As igraph is more forgiving about attribute names, it might be neccessary to simplify the them before writing to the GML file. This way we'll have a syntactically correct GML file. The following simple procedure is performed on each attribute name: first the alphanumeric characters are extracted, the others are ignored. Then if the first character is not a letter then the attribute name is prefixed with <quote>igraph</quote>. Note that this might result identical names for two attributes, igraph does not check this.
The “id” vertex attribute is treated specially.
If the id argument is not NULL then it should be a numeric
vector with the vertex ids and the “id” vertex attribute is
ignored (if there is one). If id is 0 and there is a
numeric id vertex attribute that is used instead. If ids
are not specified in either way then the regular igraph vertex ids are used.
Note that whichever way vertex ids are specified, their uniqueness is not checked.
If the graph has edge attributes named “source” or “target” they're silently ignored. GML uses these attributes to specify the edges, so we cannot write them to the file. Rename them before calling this function if you want to preserve them.
Additional arguments:
NULL or a numeric vector giving the vertex ids. See
details above.
A character scalar to be added to the
“Creator” line in the GML file. If this is NULL (the
default) then the current date and time is added.
LEDA is a library for efficient data types and algorithms. The support for the LEDA format is very basic at the moment; igraph writes only the LEDA graph section which supports one selected vertex and edge attribute and no layout information or visual attributes. See http://www.algorithmic-solutions.info/leda_guide/graphs/leda_native_graph_fileformat.html for the details of this format.
Additional arguments:
The name of the vertex attribute whose values
are to be stored in the output or NULL if no vertex
attribute has to be stored.
The name of the edge attribute whose values
are to be stored in the output or NULL if no edge attribute
has to be stored.
Gabor Csardi csardi.gabor@gmail.com
Adai AT, Date SV, Wieland S, Marcotte EM. LGL: creating a map of protein function with an algorithm for visualizing very large biological networks. J Mol Biol. 2004 Jun 25;340(1):179-90.
g <- graph.ring(10) ## Not run: write.graph(g, "/tmp/g.txt", "edgelist")