ChangeLog

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