2013-10-08 07:59 zhang
* R/parse.R: reaction graphs can now be merged
2008-10-27 07:18 zhang
* inst/doc/KEGGgraph.Rnw: rbcc in MAPK example implemented
2008-10-26 08:43 zhang
* NAMESPACE: namespace
2008-10-26 07:00 zhang
* inst/doc/KEGGgraph.Rnw: subgraph and merge graph demos finished
2008-10-26 06:25 zhang
* R/graph.R: mergeGraph returns the result explicitly
2008-10-24 17:18 zhang
* DESCRIPTION: i think it still suggested to have KEGG package
2008-10-24 17:15 zhang
* R/kegg2graph-functions.R: subtype renamed into getSubtype: small
bug in graph method
2008-10-24 17:13 zhang
* man/KEGGPathwayInfo-class.Rd, man/getDisplayName-methods.Rd:
missing items
2008-10-24 17:11 zhang
* inst/doc/KEGGgraph.Rnw: underscore package not used
2008-10-24 17:08 zhang
* tests/kegg2graph.R: kegg2graph does not load KEGG anymore
2008-10-24 17:06 zhang
* DESCRIPTION: not suggesting KEGG any more
2008-10-24 17:03 zhang
* inst/doc, inst/doc/KEGGgraph.Rnw, inst/extdata/hsa04310.xml: for
vignette
2008-10-24 16:57 zhang
* DESCRIPTION: description updated
2008-10-24 16:57 zhang
* tests/kegg2graph.R: show methods also tested
2008-10-24 16:54 zhang
* R/kegg2graph-functions.R: keggpathway show method debuged
2008-10-24 16:53 zhang
* R/kegg2graph-functions.R: pathway show method debugged
2008-10-24 16:10 zhang
* man/KEGGEdge-class.Rd, man/KEGGNode-class.Rd,
man/KEGGPathway-class.Rd, man/getDisplayName-methods.Rd,
man/getEntryID-methods.Rd, man/getKEGGID-methods.Rd,
man/getKEGGgeneLink-methods.Rd, man/getName-methods.Rd,
man/getPathwayInfo-methods.Rd, man/getReactions-methods.Rd,
man/getSubtype-methods.Rd, man/getTitle-methods.Rd,
man/getType-methods.Rd, man/getValue-methods.Rd,
man/subtypeDisplay-methods.Rd: it seems we have to add alias of
method native names to all of the files - am i right
2008-10-24 15:57 zhang
* man/KEGGEdgeSubtype.Rd, man/expandKEGGNode.Rd,
man/expandKEGGPathway.Rd, man/getKEGGgeneLink-methods.Rd,
man/getName-methods.Rd, man/getReactions-methods.Rd,
man/getRgraphvizEdgeNames.Rd, man/getSubtype-methods.Rd,
man/getTitle-methods.Rd, man/getValue-methods.Rd,
man/graphDensity.Rd, man/isHomoList.Rd,
man/kgmlFileName2PathwayName.Rd, man/parseSubType.Rd,
man/plotKEGGgraph.Rd, man/pvalue2asterisk.Rd,
man/randomSubGraph.Rd, man/subGraphByNodeType.Rd,
man/subtypeDisplay-methods.Rd: newly added docus
2008-10-24 15:57 zhang
* DESCRIPTION, man/KEGGEdgeSubType-class.Rd, man/KEGGNode-class.Rd,
man/KEGGPathway-class.Rd, man/KEGGPathwayInfo-class.Rd,
man/KEGGgraph-package.Rd, man/getEntryID-methods.Rd,
man/getKEGGID-methods.Rd, man/getType-methods.Rd: refactored in
to several files: misc for misc functions, vis for visualizations
2008-10-24 15:57 zhang
* R/graph.R, R/kegg2graph-functions.R, R/kgmlfile.R, R/misc.R,
R/vis.R: refactored in to several files: misc for misc functions,
vis for visualizations
2008-10-23 20:49 zhang
* man/getKEGGnodeData.Rd: getKEGGnode- and getKEGGedgeData
2008-10-23 20:34 zhang
* tests/testGraph.R: test whether keggorth exists before it is used
to test randomGraph
2008-10-23 20:34 zhang
* DESCRIPTION: Rgraphviz must be higher than 1.18.0 to allow
specify edge attributes in layout function
2008-10-23 17:59 zhang
* man/mergeGraphs.Rd, man/parseKGMLexpandMaps.Rd: updated docus
2008-10-23 17:54 zhang
* R/graph.R: V is unlist and as vector, to avoid the case where all
graphs have the same node number; E set simplify is FALSE, to
avoid similar bugs; null names are replaced by foo, empty names
is set as foo
2008-10-23 17:29 zhang
* R/parse.R: parseKGMLexpandMaps adds support for localdir
2008-10-23 15:08 zhang
* man/KEGGEdgeSubType-class.Rd, man/KEGGGraphics-class.Rd,
man/KEGGPathway-class.Rd: docus for classes
2008-10-23 15:00 zhang
* man/KEGGEdgeSubType-class.Rd, man/KEGGGroup-class.Rd,
man/KEGGNode-class.Rd, man/KEGGpathway2Graph.Rd,
man/parseGraphics.Rd, man/parseKGML.Rd, man/parseKGML2Graph.Rd:
updated docus
2008-10-23 15:00 zhang
* R/kegg2graph-functions.R, R/parse.R: KEGGEdgeSubtype class
renamed to KEGGEdgeSubType to avoid dupl. names with the data
'KEGGEdgeSubtype'
2008-10-23 14:32 zhang
* man/KEGGpathway2Graph.Rd, man/parseKGML.Rd,
man/parseKGML2Graph.Rd: docus for functions
2008-10-23 14:31 zhang
* man/mergeGraphs.Rd: section{Warning} should reside within note
2008-10-22 12:01 zhang
* man/mergeGraphs.Rd, man/parseKGMLexpandMaps.Rd: man pages for
mergeGraphs and parseKGMLexpandMaps
2008-10-22 10:02 zhang
* R/graph.R: lists without names (NULL) is given 'foo'
2008-10-21 14:08 zhang
* R/kegg2graph-functions.R: subtype renamed into getSubtype to keep
consistency
2008-10-20 15:45 zhang
* R/parse.R: parseKGMLexpandMaps added: it parses KGML files into
graph (genes only), expand the maps(other pathways) it contains,
downloads these maps from KGML FTP site and parse them, and at
last the graph is merged into one large graph object (though
KEGGnodeData and KEGGedgeData for now is discarded)
2008-10-20 15:26 zhang
* R/graph.R: in merging the graphs, the incoming list must be named
and NO '.' is allowed in their names
2008-10-20 12:01 zhang
* R/kegg2graph-functions.R, R/parse.R: expandKEGGPathway and
expandKEGGNode moved
2008-10-20 11:47 zhang
* R/graph.R, R/kegg2graph-functions.R, R/parse.R: functions are
moved from kegg2graph-functions to several smaller files
2008-10-20 11:45 zhang
* R/kegg2graph-functions.R: the large file is splitted to several
small files
2008-10-20 11:45 zhang
* R/graph.R: mergeGraphs moved to graph.R. Bug fix: 'graphList'
mixed into function, where it should be 'list'
2008-10-20 11:44 zhang
* R/kgmlfile.R: kgmlFileName2PathwayName moved from other file
2008-10-20 11:43 zhang
* DESCRIPTION: Unit test dependency added: RUnit as suggest added
2008-10-20 11:17 zhang
* man/getKGMLurl.Rd: Get KGML url from pathway ids
2008-10-20 11:17 zhang
* R/kgmlfile.R: functions related to KGML files
2008-10-19 10:30 zhang
* man/KEGGEdge-class.Rd, man/KEGGGroup-class.Rd,
man/KEGGNode-class.Rd, man/KEGGPathwayInfo-class.Rd,
man/KEGGReaction-class.Rd, man/KEGGgraph-package.Rd,
man/getDisplayName-methods.Rd, man/getEntryID-methods.Rd,
man/getKEGGID-methods.Rd, man/getNamedElement.Rd,
man/getSubtypeName-methods.Rd, man/getSubtypeValue-methods.Rd,
man/getType-methods.Rd, man/parsePathwayInfo.Rd,
man/parseReaction.Rd: objects first documented, not complete
2008-10-19 10:30 zhang
* man/show-methods.Rd: show methods are documented in each object
2008-10-19 10:29 zhang
* R/kegg2graph-functions.R: data names changed: KEGGNodeType,
KEGGEdgeType and KEGGEdgeSubtype dropps the plural form 's'
2008-10-19 10:28 zhang
* tests/kegg2graph.R: till the release, KEGGgraph has no namespace,
so the part testing loading/unloading removed
2008-10-19 10:28 zhang
* tests/testGraph.R: KEGGgraph library is loaded
2008-10-19 10:27 zhang
* DESCRIPTION: 'methods' dependence added
2008-10-19 09:27 zhang
* data/KEGGEdgeSubtype.csv, data/KEGGEdgeType.csv,
data/KEGGNodeType.csv: 'types' renamed into 'type' uniformly;
KEGGNodeType added
2008-10-19 09:26 zhang
* data/KEGGEdgeSubtypes.csv, data/KEGGEdgeTypes.csv: renamed
2008-10-15 06:57 zhang
* data/KEGGHumanGraphs1008.rdata,
data/KEGGTotalGraphBootstrapping.rdata: these data should not be
included in the release version of KEGGgraph, they will be
submitted into svn in working directory of miRNApathway
2008-10-15 06:45 zhang
* data/KEGGHumanGraphs1008.rdata,
data/KEGGTotalGraphBootstrapping.rdata: KEGG human graphs and its
bootstrapping statistics (data stand: 15.10.08)
2008-10-13 16:50 zhang
* R/kegg2graph-functions.R: plotKEGGgraph returns the edited graph
back so as to make further editting possible
2008-10-13 16:47 zhang
* R/kegg2graph-functions.R: global variable in subtypeDisplay,
removed
2008-10-13 15:04 zhang
* R/graph.R: functions for graph objects
2008-10-11 15:36 zhang
* R/kegg2graph-functions.R: add option sig.1 to pvalue2asterisk: to
indicate whehther drawing '.' by p=0.01
2008-10-11 14:59 zhang
* inst, inst/extdata, inst/extdata/hsa04010.xml,
inst/extdata/ko00051.xml, inst/extdata/map00260.xml: initial data
2008-10-11 14:58 zhang
* R/kegg2graph-functions.R: debug: mergeGraphs uses 'uniqueE' but
not 'uniqueE2', now the function should run without error
2008-10-11 14:57 zhang
* R/kegg2graph-functions.R: kgmlFileName2PathwayName function
added: find pathway name for KGML filename
2008-10-11 14:14 zhang
* R/kegg2graph-functions.R: pvalue2asterisk funciton added:
translate p values to common significance signs (asterisk)
2008-10-11 13:59 zhang
* R/kegg2graph-functions.R: new function 'mergeGraphs': merge a
list of graphs into one graph object. Attention: it discards
nodeData and edgeData
2008-10-11 13:44 zhang
* tests/testGraph.R: several findings of graph tested: edges must
be unique, all edges are not allowed set to NULL
2008-10-11 13:43 zhang
* R/kegg2graph-functions.R: randomSub renamed into randomSubGraph
for a consitent name with subGraph; subGraphByNodeType removes
dependency on defunct removed subKEGGgraph
2008-10-11 13:33 zhang
* R/kegg2graph-functions.R: subKEGGgraph removed: since the bug was
fixed in revision 357
2008-10-11 13:32 zhang
* R/kegg2graph-functions.R: Bug Fix: in building the graph, the
target nodes (entry2) must be unique. This fix solves the problem
the graph cannot be subsetted
2008-10-11 13:00 zhang
* R/kegg2graph-functions.R: randomSub to randomly subgraph, to test
the integratiy of a graph object
2008-10-11 12:34 zhang
* man/parseRelation.Rd: unmatched brace removed
2008-10-11 12:33 zhang
* NAMESPACE: Before the package is released the NAMESPACE is hidden
to make debugging easier
2008-10-11 12:26 zhang
* tests/testGraph.R: a trap in building graphNEL objects: nodes
without any out-edge MUST BE GIVEN a empty out edge vector,
otherwise it leads to unexpected performance
2008-10-11 12:08 zhang
* tests/kegg2graph.R: test basic operations of KEGGgraph package
2008-10-11 12:07 zhang
* tests/testGraph.R: test graph objects and attributes
2008-10-08 17:05 zhang
* man/parseEntry.Rd: updated manual for parseEntry and
parseRelation
2008-10-08 17:05 zhang
* man/parseEntry.Rd, man/parseRelation.Rd: updated manual for
parseEntry and parseRelation
2008-10-08 16:57 zhang
* man/parseEntry.Rd: manual page of parseEntry
2008-10-08 16:57 zhang
* DESCRIPTION: Description of the package
2008-10-06 15:04 zhang
* R/kegg2graph-functions.R: since subGraph seems to have problem
with my object(NA in edge, not clear yet), I have written a
subKEGGgraph and a wrapper for that subGraphByNodeType
2008-10-06 11:41 zhang
* R/kegg2graph-functions.R: getTitle and getName for pathwayInfo as
well as pathway object
2008-10-06 09:53 zhang
* R/kegg2graph-functions.R: to detemine whether there is edge or
not, edge.entryIDs' (matrix) nrow as standard, since
is.null(nrow(NA)) == TRUE
2008-10-06 09:46 zhang
* R/kegg2graph-functions.R: When building the graph, the whole
graph is built first and then sub-graphed; a check for
edge.entryIDs is added, in case of no edge (for example in
hsa00053) the code does not break, it fills all the edge list
with empty list
2008-10-06 09:25 zhang
* R/kegg2graph-functions.R: KEGGpathway2Graph: variables nodes and
edges renamed to avoid dupl. names with functions
2008-10-06 09:05 zhang
* tests: test scripts for KEGGgraph package
2008-10-06 08:31 zhang
* R/kegg2graph-functions.R: KEGGPathwayInfo is defined before
KEGGPathway, cause the latter one uses the former as component
2008-10-06 07:37 zhang
* R/kegg2graph-functions.R: MAP file: the program stops if it
detects all nodes are removed by selecting 'genesOnly' and
reminds the user to change that option
2008-10-06 07:28 zhang
* R/kegg2graph-functions.R: In KO files there're sometimes missing
entries, which leads to error in expansion. Reason for the
missing needs to be identified and until then a warning pops up
2008-10-06 07:18 zhang
* R/kegg2graph-functions.R: parseEntry function: displayName
removed (defunct)
2008-10-06 07:17 zhang
* R/kegg2graph-functions.R: parseEntry function: displayName
removed (defunct)
2008-10-05 09:56 zhang
* R/kegg2graph-functions.R: trivial spelling issue
2008-10-05 09:45 zhang
* R/kegg2graph-functions.R: checking match subtype, if not found an
error is raised;
2008-10-05 09:44 zhang
* data/KEGGEdgeSubtypes.csv: 'indirect effect' renamed into
'indirect' to be consistent with XML node; arrowhead changed in
accordance with KGML markups
2008-10-05 09:07 zhang
* R/kegg2graph-functions.R: plotKEGGgraph works now, though further
fine-tuning is needed: the trick for its work is using
layoutGraph and renderGraph interfaces in Rgraphviz package
2008-10-03 14:54 zhang
* R/kegg2graph-functions.R: subtype display is being processed, but
not finished yet
2008-10-03 14:06 zhang
* data, data/KEGGEdgeSubtypes.csv, data/KEGGEdgeTypes.csv: subtypes
and types of relations
2008-10-03 14:05 zhang
* DESCRIPTION, NAMESPACE: dependence and neccessary exporting, not
edited yet
2008-10-03 14:02 zhang
* R/kegg2graph-functions.R: debug, expandKEGGPathway mixed with
global variables; methods to extract subtype are added.
displaySubtype and plot function is not finished
2008-10-03 12:55 zhang
* R/kegg2graph-functions.R: nodeData and edgeData is saved as
environment to speed up (yes it is dramatical
improvement);bugfix: getDisplayName solves the problem of
subGraph labels; new function: parseKGML2Graph another wrapper
2008-10-03 12:02 zhang
* R/kegg2graph-functions.R: 'Subtype' in edges is now handled as
separate class; plotKEGGgraph trivial debug, allowing user
specify y value
2008-10-03 11:28 zhang
* R/kegg2graph-functions.R: getDisplayName adds method for graph,
to extract displayName in a batch; parse pathway into object
leaving out the duplicated details which are now stored in
edgeData: relation types, subtype name and value
2008-10-03 10:57 zhang
* R/kegg2graph-functions.R: Debug:KEGGpathway2Graph global scope
variable contanminated(pathway by keggPathway, twice). expand
function is integrated into KEGGpathway2Graph function
2008-10-03 10:20 zhang
* R/kegg2graph-functions.R: expandKEGGPathway function added:
expand entry into genes
2008-10-03 08:46 zhang
* R/kegg2graph-functions.R: KEGGpathway2Graph function added: it
converts a KEGGPathway object to graphNEL object, saving nodes
and edges in edgeData and nodeData perspectively. So far
expandGenes is not implemented
2008-10-02 16:35 zhang
* R/kegg2graph-functions.R: new classes 'KEGGPathway' and
'KEGGPathwayInfo' added and their basic functions implemented;
tested by clearing and importing again
2008-10-02 09:44 zhang
* R/kegg2graph-functions.R: KEGGNode refactored into KEGGNode
containing KEGGGraphics
2008-10-01 16:43 zhang
* ., DESCRIPTION, NAMESPACE, R, R/kegg2graph-functions.R, man,
man/KEGGEdge-class.Rd, man/KEGGGroup-class.Rd,
man/KEGGNode-class.Rd, man/KEGGPathwayInfo-class.Rd,
man/KEGGReaction-class.Rd, man/KEGGgraph-package.Rd,
man/getDisplayName-methods.Rd, man/getEntryID-methods.Rd,
man/getKEGGID-methods.Rd, man/getNamedElement.Rd,
man/getSubtypeName-methods.Rd, man/getSubtypeValue-methods.Rd,
man/getType-methods.Rd, man/parseEntry.Rd,
man/parsePathwayInfo.Rd, man/parseReaction.Rd,
man/parseRelation.Rd, man/show-methods.Rd: Rpackage to build
graph objects from KEGG pathway
