CHANGES IN VERSION 3.23 ------------------------ o Kegg-related functionalities have been removed. CHANGES IN VERSION 3.15 ------------------------ o plotKegg() has been deprecated. It will be removed from the package in upcoming versions. CHANGES IN VERSION 3.4 ------------------------ o Added argument 'downloadFile' to fea_david() to choose whether to save the analysis results to the current directory o DAVID now requires https. This causes errors in some systems. A (hopefully) temporary solution is to install some certificates locally. See RDAVIDWebService help: https://support.bioconductor.org/p/70090/#72226 CHANGES IN VERSION 3.2 ------------------------ NEW FEATURES o HTML vignette o Bipartite network: Nodes are now circles and squares (only available for "static" plot) o PlotGoAncestors: added argument nCharTerm o clustersDistance: added argument 'clustMethod' and set "average" as default clustering method. o GO evidence: Added argument to fea_topGO (new data object available: GOEvidenceCodes) o Added argument vExprColors to functionalNetwork. o Vertex size now allows to set a value for each gene. BUGFIXES o fea2incidMat: filter negative values CHANGES IN VERSION 3.0 ------------------------ NEW FEATURES o Graphical User Interface (GUI) o New FEA tools: topGO and GAGE (GSEA) o Plot gene expression (up/down) in the functional networks (Available since devel. version 2.1) o plotGoAncestors, plotKegg INTERFACE CHANGES o Functions renamed or replaced: o toMatrix/adjMatrix: fea2incidMat o plotMetagroupsDistance: clusterDistance o query_gtLinker & getResults_gtLinker: fea_gtLinker & fea_gtLinker_getResults o query_david & getResults_david: fea_david & format_david o report_gtLinker & report_david: FGNet_report o intersectionNetwork: is now included in functionalNetwork CHANGES IN VERSION 2.1 ------------------------ NEW FEATURES o Expression in functionalNetwork: It is now possible to plot gene expression (up/down) in the network. o plotGoAncestors: New function. o report: Added option to show only the most specific GO terms (tree leaves: terms at the bottom of the ontology). Kegg pathway plot can now be plotted and saved locally. o Added p-value stats to clusters matrix. o Side colors added to metagroups heatmap. o toMatrix: added argument sepChar, legendPrefix and filterOperator. Attribute and threshold renamed to filterAttribute and filterThreshold. o functionalNetwork: added arguments plotIntersectionNetwork,plotTitleSub. o getResults_gtLinker: added argument organism (adds the prefix to kegg id). o getResults_david: inputFileLocation renamed to fileName BUG FIXES o GO ontology plot: now done locally through plotGoAncestors. o toMatrix: Accepts characters in cluster column (provides more flexibility with non-clustered/modular FEA and support to build term-term and term-genes networks). Arguments: legendMg renamed to legendText. CHANGES IN VERSION 2.0 ------------------------ NEW FEATURES o The networks can now be plotted for terms in addition to genes. o In the report, clicking on the plots allows to see the plot at full size next to the terms table (if the screen resolution allows it). o ToMatrix(): Added arguments 'key' (to choose either genes or terms) and 'removeFiltered' terms. Renamed main argument (geneTermSets) to 'results'. o IntersectionNetwork() shows a warning if there is no intersection. Added argument 'plotAllMg' to allow choosing wether to plot unconnected metagroups or not. o FunctionalNetwork() changed the two main arguments to a single one, which is the raw output from toMatrix() (a list with names: c("metagroupsMatrix", "gtSetsMatrix", "filteredOut")). Added arguments: 'eColor' to provide the edges color, and 'weighted' to draw the edge width according to the number of shared gene-term sets. o Reports: Added argument 'downloadGOtree' to allow choosing wether to download the go term trees png (slower) or just provide the link to the web tool. BUG FIXES o functionalNetwork() now correctly writes either "cl" or "mg" in the legend. CHANGES IN VERSION 1.3.1 ------------------------ NEW FEATURES o adjMatrix() has been renamed to toMatrix() o GO png trees are now automatically downloaded when generating the report o functionalNetwork: metagroup/cluster legend order has been changed to alphabetical BUG FIXES o Minor bug fixes CHANGES IN VERSION 1.2 ------------------------ NEW FEATURES o Query David through web service (RDAVIDWebService): Avoids limitations of API interface o Added argument KeepColors to functionalNetwork and intersectionNetwork: Keeps the same color for each group even if some are filtered out. o Added argument geneLabels to getResults_david: Allows to replace the IDs for a gene name/symbol in the plots BUG FIXES o Minor bug fixes CHANGES IN VERSION 1.1.1 ------------------------ BUG FIXES o query_david: Checks whether the server accepted the query o MAN pages using query_david: Reduced yeast example to 15 genes. In windows, with the whole gene list, the server returns "Error: Expectation failed". CHANGES IN VERSION 1.0.0 ------------------------ NEW FEATURES o Package released