NEWS

FGNet 3.26

plotKegg() has been deprecated. It will be removed from the package in upcoming versions.

Added argument 'downloadFile' to fea_david() to choose whether to save the analysis results to the current directory
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

HTML vignette
Bipartite network: Nodes are now circles and squares (only available for "static" plot)
PlotGoAncestors: added argument nCharTerm
clustersDistance: added argument 'clustMethod' and set "average" as default clustering method.
GO evidence: Added argument to fea_topGO (new data object available: GOEvidenceCodes)
Added argument vExprColors to functionalNetwork.
Vertex size now allows to set a value for each gene.

Graphical User Interface (GUI)
New FEA tools: topGO and GAGE (GSEA)
Plot gene expression (up/down) in the functional networks (Available since devel. version 2.1)
plotGoAncestors, plotKegg

Expression in functionalNetwork: It is now possible to plot gene expression (up/down) in the network.
plotGoAncestors: New function.
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.
Added p-value stats to clusters matrix.
Side colors added to metagroups heatmap.
toMatrix: added argument sepChar, legendPrefix and filterOperator. Attribute and threshold renamed to filterAttribute and filterThreshold.
functionalNetwork: added arguments plotIntersectionNetwork,plotTitleSub.
getResults_gtLinker: added argument organism (adds the prefix to kegg id).
getResults_david: inputFileLocation renamed to fileName

GO ontology plot: now done locally through plotGoAncestors.
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.

The networks can now be plotted for terms in addition to genes.
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).
ToMatrix(): Added arguments 'key' (to choose either genes or terms) and 'removeFiltered' terms. Renamed main argument (geneTermSets) to 'results'.
IntersectionNetwork() shows a warning if there is no intersection. Added argument 'plotAllMg' to allow choosing wether to plot unconnected metagroups or not.
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.
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.

adjMatrix() has been renamed to toMatrix()
GO png trees are now automatically downloaded when generating the report
functionalNetwork: metagroup/cluster legend order has been changed to alphabetical

Query David through web service (RDAVIDWebService): Avoids limitations of API interface
Added argument KeepColors to functionalNetwork and intersectionNetwork: Keeps the same color for each group even if some are filtered out.
Added argument geneLabels to getResults_david: Allows to replace the IDs for a gene name/symbol in the plots

query_david: Checks whether the server accepted the query
MAN pages using query_david: Reduced yeast example to 15 genes. In windows, with the whole gene list, the server returns "Error: Expectation failed".