# GeneTonic 1.2.0 ## Other notes * Added an additional mechanism for safe fails when not finding the GO Term and searching for the definition - this could happen e.g. when the term becomes outdated and is removed from the `GO.db` package, or also mistyped if entered by hand at some point. # GeneTonic 1.0.0 ## Other notes * `GeneTonic` has become a part of Bioconductor! # GeneTonic 0.99.0 ## Other notes * `GeneTonic` is now submitted to Bioconductor! # GeneTonic 0.10.0 ## New features * The functions for comparing different `res_enrich`, namely `gs_radar`, `gs_summary_overview_pair`, and `gs_horizon` were internally rewritten to accept correctly the comparison elements * The vignette now covers completely the usage cases, with the full description of the user interface of `GeneTonic` * The introductory tours are available for all the main panels of `GeneTonic`. Feel free to try them out! ## Other notes * Some widgets have been added in the UI of `GeneTonic` to enable finer control of the output aspect * Examples and unit tests have been further expanded, with better messages for checking progress * `check_colors` verify that color palettes are correctly provided * Info on `GeneTonic` is now provided with modal dialog windows, rather than in a separate tab * The tab names in the main app were slightly edited to better describe their content * The info boxes are now shown with a uniform style, based on the `bs4Card` UI element * The UI elements have now a better spacing throughout the different tabs * Soon the package will be submitted to Bioconductor! # GeneTonic 0.9.0 ## New features * `GeneTonic` sports a blazing new hex sticker - say bye to the original draft! * The overview DT `datatable`s has some styling with color bars - e.g. for DE results - to enhance the visual perception of numeric values (e.g. log2FoldChange) * `gs_heatmap` can now take a custom list of gene identifiers (when no geneset is passed) * The color palettes in enrichment maps now respect the values and the range specified of the numeric values to be used for mapping to colors * `gs_mds` is now optionally returning a data.frame, to be further used for custom plotting or downstream processing * `gs_summary_overview` now has coloring enabled by the variable of choice ## Other notes * The UI has received some restyling (e.g. in the choice of the icons for the dropdown menus, or the name of some buttons) * Added tour contents for most of the functionality * Added link to the demo instance * Added examples for overlap functions, gene info buttons, map2color, and deseqresult2df * Extended documentation of some parameters * Some functions have gained an alias for calling them: `gs_spider` is equivalent to `gs_radar`, and `gs_sankey` is equivalent to `gs_alluvial` # GeneTonic 0.8.0 ## New features * `GeneTonic` now delivers bundled example objects to make examples and tests slim * `gs_volcano` can now plot points by different colors according to the columns of interest * `GeneTonic` has a fully fledged manual describing its functionality and user interface ## Other notes * Now using ids for genes and genesets for exchanging information in the app * Added examples for all functions * Most tabs have working tours - anchor and text elements # GeneTonic 0.7.0 ## New features * Introduced a uniform interface for calculating different similarity/distance matrices. This enables the usage in the different functions that might need such matrices for further downstream processing (e.g. `enrichment_map()`, `gs_mds()`) * First appearance of `gs_dendro()` to display distance matrices with some visualization sugar, as an alternative to other methods * The `n_gs` and `gs_ids` are exposed to more functions to enable custom subsets of the enrichment results to be inspected # GeneTonic 0.6.0 ## New features * `gs_heatmap` now relies on `ComplexHeatmap`, to avoid the issues with Shiny of not displaying the outputs in the app, and enabling a comfortable heatmap annotation * Many functions gain the possibility to pass a set of custom geneset identifiers to be added to the top N sets (default): among these, `gs_mds`, `gs_volcano` (parameter: `gs_labels`), `gs_alluvial`, `ggs_network`, `enrichment_map`, and `enhance_table` (using `gs_ids`) ## Other notes * `gs_ggheatmap` got renamed to `gs_scoresheat` * The report generated from the bookmarked content is expanded in its default content # GeneTonic 0.5.0 ## New features * `GeneTonic` now enforces a format for `res_enrich`, and provides some conversion functions, `shake_*()`. Requirements are specified in the documentation, if an appropriate converter does not (yet) exist. * The reporting feature is active to some extent on the bookmarked content. # GeneTonic 0.4.0 ## New features * Added functionality for bookmarking * Bookmarking can work (PoP) by pressing a key (left control)! * `gene_plot` can enforce a plot type overriding the default based on the number of samples per condition * `GeneTonic` uses now `bs4Dash` and many of its nice features, replacing the previous implementation based on `shinydashboard` # GeneTonic 0.3.0 ## Other notes * Rearranging the order of parameters to harmonize it across functions, and uniforming similarly called parameters # GeneTonic 0.2.0 ## New features * added geneset scoring calculation and corresponding heatmap # GeneTonic 0.1.0 ## New features * much of the functionality available, in a proof of concept format # GeneTonic 0.0.1 ## New features * backbone of the project started!