ActivePathways 1.1.1

Major Changes

Added an option for the colours specified in the “custom_colors” parameter to be provided in any order, as long as the vector “names()” match the column names of the “scores” matrix.
Fixed an error where the “combined” contribution label was absent from the legend.pdf ActivePathways output file.

Updated the filtering procedure of gene sets in the GMT file when a custom gene background is provided. Given a background gene list, the GMT gene sets are first modified to only include the genes of the background list, and second, the gene sets are filtered by gene set size. Gene sets lacking any genes from the background list are removed. This update will result in a more lenient multiple testing correction in analyses with a custom background gene list.

Added three new parameters to ActivePathways and prepareCystoscape functions. These include “color_palette”, “custom_colors” and “color_integrated_only” to provide more options for node coloring in Cytoscape.

Renamed package to ActivePathways from activePathways for consistency with function and publication
Added new function export_as_CSV(res, file_name) to save data in spreadsheet-friendly formats
Updated README-file with an actionable step-by-step tutorial
Changed logic of creating files for Enrichment Map: the user can provide the parameter “cytoscape.file.tag” for creating the required files. If the parameter is NA (default), no files are created. No directories are created.
Removed the parameter “return.all” as it was redundant with the parameter “significance”.
Removed the parameter “reanalyze” to simplify the package and leave the structuring of results up to the user.
Removed the dependency on the R package metap. As a result, only Fisher’s and Brown’s p-value merging options are available.
Updated the vignette that now describes the ActivePathways package as well as the following steps of visualising results as enrichment maps in Cytoscape.