NEWS

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pathview 1.43.1

• add org.EcK12.eg.db to Suggests for BioC build check
• korg now include 9767 KEGG species or 1485 new species beyond 2022.

pathview 1.37.1

• fix bug in download.kegg caused by recent change in kegg rest API urls (http to https).
• korg now include 8282 KEGG species or 1449 new species beyond 2020.

pathview 1.31.3

• fix bug in mol.sum with single gene data reported by easygsea. Similarly add drop=F to a few other lines in mol.sum and node.map.

pathview 1.31.2

• solve the check error due to the change related to KEGGEdgeSubtype in KEGGgraph package (version 1.51.1).

pathview 1.31.1

• korg now include 6833 KEGG species or 1588 new species beyond 2017.

pathview 1.29.1

• developmental version now available on GitHub at: https://github.com/datapplab/pathview
• fixed warning on "requireNamespace(pkg.name)" in geneannot.map.R and sim.mol.data.R. Now "import" from org.Hs.eg.db, instead of "suggest" it. Also import more functions and class from AnnotationDbi.
• prevented potential error caused by class(exprs) == "data.frame" or "class()==" if conditions in multiple functions. class(exprs) now returns a vector of length 2, which caused the error.

pathview 1.23.3

• fix error and warning cause by geneannot.map() function. change if(in.type == out.type) to if(all(in.type == out.type)). change biocLite installation to BiocManager::install. make similar changes in sim.mol.data() function.
• update NAMESPACE file on importFrom lines on AnnotationDbi and BiocManager.

pathview 1.18.2

• korg now include 5245 KEGG species. To speed up pathview package loading, an updated version of korg is now checked out from Pathview Web server only when it is acutally used and needed.

pathview 1.17.7

• updated combineKEGGnodes.R, i.e. changed the stop error to a warning message when a group node include different node types, i.e. both gene and compound. This problematic KEGG node definition does exist in pathway 04136 Autophagy - other, and caused error when calling pathview with kegg.native = F.
• fixed bug in mol.sum introduced at 1.15.1, i.e. indexing using which(eff.idx). This problem only affect direct call of mol.sum with sum.method other than "sum" and "mean".

pathview 1.17.1

• major expansion in korg, which now include both KEGG and NCBI taxonomy IDs, two more gene ID types, i.e. NCBI protein and uniprot IDs. In addition, Entrez or NCBI Gene IDs are discontinued for most prokaryotes.
• korg now include 4800 KEGG species, in the meantime, an updated version of korg is now checked out from Pathview Web server each time pathview package is loaded.

pathview 1.15.1

• fixed bug in node.map on single row/mapped data, and in mapped row numbers.

pathview 1.10.2

• fixed problem that no node mapped when one gene/protein ID maps to multiple Entrez Gene ID (like Enzyme IDs): id2eg call with unique.map=F.

pathview 1.10.1

• fix bug in reaction2edge function, which throw error for a few metabolic pathways with no multi-node reaction group (examples including 00072, 00100).

pathview 1.9.3

• pathview can accept a vector of multiple pathway ids, and map/render the user data onto all these pathways in one call.
• one extra column "all.mapped" was added to pathview output data.frames as to show all the gene/compound IDs mapped to each node.
• add geneannot.map as a generic function for gene ID or annotation mapping.
• sim.mol.data now generate data with all major gene ID types for all 19 species in bods, not just human.
• download.kegg now let the user to choose from xml, png or both file types to download for each input pathway. In the meantime, it uses the KEGG REST API instead of the classical KEGG download links. All potential pathways including the general pathways can be downloaded this way.
• solve the redundant import from graph package.
• import specific instead of all functions from XML package.

pathview 1.9.1

• solve the install error due to the recent change in KEGGgraph package.

pathview 1.5.4

• adjust run-time messages into 3 consistent classes: Info (on progress), Note and Warning.
• include paths.hsa data, the full list of human pathway ID/names from KEGG, as to help user specify target pathways when calling pathview.
• updated korg to included over 80 newly added species, such as sheep, apple, mandarin orange etc. Pathview can work with 3050 species now.
• adjust the definitions of 7 arguments for pathview function: discrete, limit,bins, both.dirs, trans.fun, low, mid, high. These used to be a list of two logical elements with "gene" and "cpd" as the names. They can be vectors of two or one element(s) now. This makes pathview easier to use now.
• Vigette has been reformatted: add a Citation section, and some example on reading user data into R, fix a few typos.

pathview 1.4.2

• fixed bug in render.kegg.node function, which generates black lines in some nodes of multiple sample view.

pathview 1.3.6

• ajusted node x coordinate by +0.5 to better fit the color blocks in 2 layer native kegg views.

pathview 1.3.4

• updated bods to included an extra column of id.type, the default gene ID type.

pathview 1.2.4

• updated korg to included over 600 newly added species. Pathview can work with 2970 species now.
• Make returned values from pathview, keggview.native and keggview.graph functions invisible.

pathview 1.2.3

• Fixed bug in node.map function, which produces 0 values when all multiple genes in a node are NA's.

pathview 1.2.2

• Fixed bug in mol.sum function, which generates "incorrect number of dimension" or NA's when sum.method="median" etc.

pathview 1.2.1

• 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.

pathview 1.1.7

• Graphviz view can automatic choose different types of legends, either on nodes, edges or both depending on the specific pathways.
• Vigette has been reformatted: the "Quick start" section added

pathview 1.1.6

• 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.
• Vigette has been reformatted: Data integration section splitted into multiple sub-sections.

pathview 1.1.5

• 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.

pathview 1.1.3

• Pathview paper published in Bioinformatics

pathview 1.0.0

• Initial release with Bioconductor
• Main function: pathview
• 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