o将运行时消息调整为3个一致的类:Info (on progress)， Note和Warning。O包含路径。hsa数据，来自KEGG的人类路径ID/名称的完整列表，以帮助用户在调用pathview时指定目标路径。O更新了korg，新增了80多个物种，如绵羊、苹果、柑桔等。Pathview现在可以使用3050个物种。O调整pathview函数的7个参数的定义:discrete, limit,bins，两者。dirs,反式。有趣，低，中，高。这曾经是一个包含两个逻辑元素的列表，以“gene”和“cpd”作为名称。现在它们可以是两个或一个元素的向量。这使得路径视图现在更容易使用。 o Vigette has been reformatted: add a Citation section, and some example on reading user data into R, fix a few typos. VERSION 1.4.2 ------------- o fixed bug in render.kegg.node function, which generates black lines in some nodes of multiple sample view. VERSION 1.3.6 ------------- o ajusted node x coordinate by +0.5 to better fit the color blocks in 2 layer native kegg views. VERSION 1.3.4 ------------- o updated bods to included an extra column of id.type, the default gene ID type. VERSION 1.2.4 ------------- o updated korg to included over 600 newly added species. Pathview can work with 2970 species now. o Make returned values from pathview, keggview.native and keggview.graph functions invisible. VERSION 1.2.3 ------------- o Fixed bug in node.map function, which produces 0 values when all multiple genes in a node are NA's. VERSION 1.2.2 ------------- o Fixed bug in mol.sum function, which generates "incorrect number of dimension" or NA's when sum.method="median" etc. VERSION 1.2.1 ------------- o Fixed bug in "missing red disease gene node labels" in diease pathways. To avoid interfering with node coloring, set all disease gene labels to black instead. VERSION 1.1.7 ------------- o Graphviz view can automatic choose different types of legends, either on nodes, edges or both depending on the specific pathways. o Vigette has been reformatted: the "Quick start" section added VERSION 1.1.6 ------------- o Pathview can plot/integrate/compare multiple states/samples in the same graph. Several functions and data objects are revised: including pathview, keggview.native, keggview.graph, render.kegg.node etc. New section on multiple state data with working exampleshas been added. o Vigette has been reformatted: Data integration section splitted into multiple sub-sections. VERSION 1.1.5 ------------- o Pathview works with species where default KEGG gene ID is not Entrez Gene. Several functions and data objects are revised: including pathview, node.map, sim.mol.data, kegg.species.code, korg. New section on KEGG species and Gene ID usage with working exampleshas been added. VERSION 1.1.3 ------------- o Pathview paper published in Bioinformatics VERSION 1.0.0 ------------- o Initial release with Bioconductor o Main function: pathview o Four functional modules: -Downloader: download.kegg; -Parser: node.info, combineKEGGnodes, reaction2edge; -Mapper: node.map, eg2id, id2eg, cpdkegg2name, cpdname2kegg, cpd2kegg, cpdidmap, kegg.species.code, mol.sum, sim.mol.data; -Viewer: keggview.native, keggview.graph, node.color, col.key, wordwrap, strfit