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