03-main: Converting GPML FIles to Igraph Objects
In WayFindR: Computing Graph Structures on WikiPathways
XMLtoIgraph R Documentation
Converting GPML FIles to Igraph Objects
Description
Takes an XML file, either GPML from WikiPathways, or KGML from KEGG,
extracts the entities therein,
and makes minor adjustments necessary to convert it into an
igraph object. Along the way, it assigns a consistent set
of colors, line types, and shapes.
Usage
GPMLtoIgraph(xmldoc, returnLists = FALSE, debug = FALSE)
KGMLtoIgraph(xmldoc, returnLists = FALSE, debug = FALSE)
nodeLegend(x, graph)
edgeLegend(x, graph)
Arguments
xmldoc
Either the name of an XML file meeting the
specifications of the appropriate markup language (GPML or KGML), or
an object of class XMLInternalDocument obtained by running such
a file through the xmlParseDoc function of the XML
package.
returnLists
A logical value; should the return value
include the node list and edge list matrices?
debug
A logical value; should debugging progress information be
printed? Probably best to leave it equal to FALSE.
x
A character string, such as "topleft" indicating where
to place the legend.
graph
An igraph object as produced by the
functionGPMLtoIgraph.
Details
GPMLtoIgraph and KGMLtoIgraph are the main functions of
the WayFindRpackage. They achieve the primary goal of
converting pathways from one of the biological graph XML file formats
into a mathematical graph, in the format defined by the
igraph package. At that point, we can apply a wide
variety of graph algorithms from computer science in order to
"compute on biological pathways".
The implementation of these functions relies on the utility functions
described in gpml-utility or kgml-utility.
Briefly, the first algorithm starts by collecting all nodes
(DataNodes in GPML) and edges (Interactions in GPML)
from the GPML input file. However, GPML includes two other structures
with (semantic) biological meaning. First, the GPML description
includes the idea of an (invisible) "Anchor" that allows one
edge to point to another edge. We expand those invisible target
locations into full-fledged nodes in the final graph. Second, GPML
includes "Groups" that represent protein complexes or sets of
closely related genes. In WayFindR, we represent such groups
as their own nodes in the final graph, and add "contained" edges
linking in the group members. The transformations of Anchors and
Groups do not change the fundamental topology (in particular, the
existence of cycles) of the resulting graph.
Further, GPML includes non-semantic features (including "Labels"
and "Shapes") that are (mis)used by some pathway authors as the
targets of edges. WayFindR converts any targeted non-semantic
features into nodes in order to preserve as much information as
possible from the original pathway in WikiPathways.
The KGML algorithm is similar in structure, burt has to deal with the
diferent underlying sdtructure of th KGML specification. Tghei files
contina three kinds of entities: Entry, Relation, and
Reaction. An Entry becoemes a vertex. It can be a gene,
a map (a link to another pathway), a group (as above, except that the
members of the group are stored as an entity called a
Component within the group Entry), an ortholog (a KEGG-defined
set of genes that are teh "same" across species), or a compound
(subdivided into compounds, glycans, or drugs, all of which we view as
"SmallMolecules" analogous to what GPML calls a metabolite). A
Relation is an edge that usually connects genes, but we must
map the terminology annotating edge types into the MIM space
defining biological edges. Finally, a Reaction is an edge
between compounds, which has no real analog in the WikiPathways
universe. The only "type" associated with a reaction is whether it is
"reversible" or "irreversible".
Value
The GMLtoIgraph function usually returns an igraph
object that represents the pathway defined by the input
xmlfile. If the argument returnLists = TRUE, then it
returns a list containing three components; graph is the
igraph object, nodes is a data frame containing node
information where each row is a node, and edges is a matrix
containing edge information where each row is an edge. The node and
edge information can be used to reproduce the graph in any network or
graph visualization tool that accepts such matrices to describe the
graph. The nodes data frame includes columns for color
and shape, and the edges data frame includes columns for
color and lty that are recognized and used by the
plot.igraph function.
Both nodeLegend and edgeLegend invisibly return the same
value that is returned by the legend function that is
used in the implementation.
Author(s)
Kevin R. Coombes krc@silicovore.com,
Polina Bombina pbombina@augusta.edu
Examples
xmlfile <- system.file("pathways/WP3850.gpml", package = "WayFindR")
graf <- GPMLtoIgraph(xmlfile)
set.seed(13579)
L <- igraph::layout_with_graphopt
plot(graf, layout=L)
nodeLegend("topleft", graf)
edgeLegend("bottomright", graf)
WayFindR documentation built on Feb. 23, 2025, 3:01 a.m.
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| XMLtoIgraph | R Documentation |
Converting GPML FIles to Igraph Objects
Description
Takes an XML file, either GPML from WikiPathways, or KGML from KEGG,
extracts the entities therein,
and makes minor adjustments necessary to convert it into an
igraph object. Along the way, it assigns a consistent set
of colors, line types, and shapes.
Usage
GPMLtoIgraph(xmldoc, returnLists = FALSE, debug = FALSE)
KGMLtoIgraph(xmldoc, returnLists = FALSE, debug = FALSE)
nodeLegend(x, graph)
edgeLegend(x, graph)
Arguments
xmldoc |
Either the name of an XML file meeting the
specifications of the appropriate markup language (GPML or KGML), or
an object of class |
returnLists |
A logical value; should the return value include the node list and edge list matrices? |
debug |
A logical value; should debugging progress information be printed? Probably best to leave it equal to FALSE. |
x |
A character string, such as "topleft" indicating where to place the legend. |
graph |
An |
Details
GPMLtoIgraph and KGMLtoIgraph are the main functions of
the WayFindRpackage. They achieve the primary goal of
converting pathways from one of the biological graph XML file formats
into a mathematical graph, in the format defined by the
igraph package. At that point, we can apply a wide
variety of graph algorithms from computer science in order to
"compute on biological pathways".
The implementation of these functions relies on the utility functions
described in gpml-utility or kgml-utility.
Briefly, the first algorithm starts by collecting all nodes
(DataNodes in GPML) and edges (Interactions in GPML)
from the GPML input file. However, GPML includes two other structures
with (semantic) biological meaning. First, the GPML description
includes the idea of an (invisible) "Anchor" that allows one
edge to point to another edge. We expand those invisible target
locations into full-fledged nodes in the final graph. Second, GPML
includes "Groups" that represent protein complexes or sets of
closely related genes. In WayFindR, we represent such groups
as their own nodes in the final graph, and add "contained" edges
linking in the group members. The transformations of Anchors and
Groups do not change the fundamental topology (in particular, the
existence of cycles) of the resulting graph.
Further, GPML includes non-semantic features (including "Labels"
and "Shapes") that are (mis)used by some pathway authors as the
targets of edges. WayFindR converts any targeted non-semantic
features into nodes in order to preserve as much information as
possible from the original pathway in WikiPathways.
The KGML algorithm is similar in structure, burt has to deal with the
diferent underlying sdtructure of th KGML specification. Tghei files
contina three kinds of entities: Entry, Relation, and
Reaction. An Entry becoemes a vertex. It can be a gene,
a map (a link to another pathway), a group (as above, except that the
members of the group are stored as an entity called a
Component within the group Entry), an ortholog (a KEGG-defined
set of genes that are teh "same" across species), or a compound
(subdivided into compounds, glycans, or drugs, all of which we view as
"SmallMolecules" analogous to what GPML calls a metabolite). A
Relation is an edge that usually connects genes, but we must
map the terminology annotating edge types into the MIM space
defining biological edges. Finally, a Reaction is an edge
between compounds, which has no real analog in the WikiPathways
universe. The only "type" associated with a reaction is whether it is
"reversible" or "irreversible".
Value
The GMLtoIgraph function usually returns an igraph
object that represents the pathway defined by the input
xmlfile. If the argument returnLists = TRUE, then it
returns a list containing three components; graph is the
igraph object, nodes is a data frame containing node
information where each row is a node, and edges is a matrix
containing edge information where each row is an edge. The node and
edge information can be used to reproduce the graph in any network or
graph visualization tool that accepts such matrices to describe the
graph. The nodes data frame includes columns for color
and shape, and the edges data frame includes columns for
color and lty that are recognized and used by the
plot.igraph function.
Both nodeLegend and edgeLegend invisibly return the same
value that is returned by the legend function that is
used in the implementation.
Author(s)
Kevin R. Coombes krc@silicovore.com, Polina Bombina pbombina@augusta.edu
Examples
xmlfile <- system.file("pathways/WP3850.gpml", package = "WayFindR")
graf <- GPMLtoIgraph(xmlfile)
set.seed(13579)
L <- igraph::layout_with_graphopt
plot(graf, layout=L)
nodeLegend("topleft", graf)
edgeLegend("bottomright", graf)
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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