版本1.37.1（2017-07-20） + PathView版本1.37.0（2017-07-12）中使用的导出ParsePathwayInfo +清理名称空间文件文件 + UPDATE retive refievekgml +更好的错误报告，以防空kgml kgml文件版本1.35.1（2017-06-19） +感谢AR3513@bioc的报告，我们修复了XML :: XMLChildren引起的警告，如果XMLNODE没有孩子。现在，通过其他内部功能明确测试了此类情况。版本1.27.2（2015-05-25） +仅从图导入功能的子集。它应该在此处解决：http：//stackoverflow.com/questions/30428860/proper-use-op-optional-package-features-and-and-dependencies。版本1.27.1（2015-05-04） +多亏了Anders Ellern Bilgrau的输入，固定了一个错误，该错误造成了绘图架对象的多个边缘版本1.21.1（2013-10-17）---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------》即现在可以处理空对象，o keggpathway2graph消除了重复的边缘，以便parsekgml2dataframe不会失败。（感谢Paul Shannon的Bug报告）o Paul Shannon在版本1.19.0的Kegggraph更改中添加了一组运行测试------------------------------------------------------------------------------------------------o感谢Martin Morgan的建议，Kegggraph Package的Devel版本使用了奇怪的第二个数字版（1.19.0）版本1.18.0中的更改--------------------------------------------------------------------------------------------- o keggpathway2Reactiongraph的变化允许用户合并反应图，例如路径图，版本1.18.1 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------O Parsekgml2DataFrame接受选项“反应”，将反应包括在解析数据中。版本1.18.1中的更改​​-------------------------------------------------------------------------------------------------------------------o KEGGpathway2reactionGraph prints warnings and returns NULL when the pathway does not contain any reaction CHANGES IN VERSION 1.11.1 ------------------------- o The colorectalcancerSPIA dataset has been compressed with R CMD build --resave-data CHANGES IN VERSION 1.9.2 ------------------------ o Update getKGMLurl and retrieveKGML to get KGML files from HTTP pages instead of from the FTP server, which is from July 2011 only open to subscribed users. The KEGG database needs support, and users of KEGGgraph could also support by subscribing to the FTP service. CHANGES IN VERSION 1.9.1 o Add parseKGML2DataFrame function. This function is table to convert the KGML file into a data frame recording nodes and edges in one step. For help use '?parseKGML2DataFrame' in R command line. CHANGES IN VERSION 1.9.0 ------------------------- o Auto version bumping by Bioconductor updates CHANGES IN VERSION 1.3.2 ------------------------ o'indirect' subtype has been renamed into 'indirect effect', KEGGEdgeSubtype.csv file makes modifications. Thanks Siyuan Zhang for reporting the bug. CHANGES IN VERSION 1.3.1 ------------------------- o KEGG FTP server is again changed, from 'ftp://ftp.genome.jp/pub/kegg/xml/kgml/non_metabolic/organisms' to 'ftp://ftp.genome.jp/pub/kegg/xml/kgml/non-metabolic/organisms'. Note the minus and underscore. Thanks Tim Fraser and Marc Carlson for reporting. CHANGES IN VERSION 1.1.13 ------------------------- o Add Makefile to facilitate the check/install, and the try-download mechanism of retrieveKGML is documented in the vignette. CHANGES IN VERSION 1.1.12 ------------------------- o Update due to the change of FTP sites of KEGG website. Now pathways are stored separatedly depending whether they are metabolic pathways or not. KEGGgraph is now able to automatically download files. CHANGES IN VERSION 1.1.9 ------------------------ o KEGGgraph software supports multiple substrates/products in KGML reaction from version 1.1.9. Earlier versions only read the first pair. Code name 'Kitty', thanking report from Plaimas Kitiporn, DKFZ. CHANGES IN VERSION 1.1.1 ------------------------ o Improved render of KEGG pathway graphs with new interface of Rgraphviz, nodeRenderInfo parameter renamed into nodeRenderInfos to avoid conflict CHANGES IN VERSION 0.8.6 ------------------------ o 'KEGGpathway2reactionGraph' added to parse compound reaction network into graph. Documentationss updated CHANGES IN VERSION 0.8.5 ------------------------ o Help pages updated with detailed examples, 'getReactions' series of functions are tested. CHANGES IN VERSION 0.8.4 ------------------------ o 'group' entries (complexes in most cases) are also parsed and expanded by default now. CHANGES IN VERSION 0.8.3 ------------------------ o 'Collate' field added in DESCRIPTION file CHANGES IN VERSION 0.8.2 ------------------------ o 'mergeKEGGgraph' function added to keep KEGGnodeData and KEGGedgeData even after merging graphs CHANGES IN VERSION 0.8.1 ------------------------ o 'subKEGGgraph' function added to maintain KEGGnodeData and KEGGedgeData even after subsetting graphs CHANGES IN VERSION 0.8.0 ------------------------ o Initial release of 'KEGGgraph' package