NEWS.md

In federicomarini/GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

GeneTonic 2.99.0

Other notes

• The transition to the functions available in the mosdef Bioconductor is complete, with the original functions now being deprecated. This applies to goseqTable() (now replaced by mosdef::run_goseq()), which has now been made faster and more robust in its functionality and in the ways it can be executed
• The gene plot widgets now also use the gene_plot() function from mosdef, instead of the previous ggplotCounts() function - gene_plot() is more flexible and has more options to control the behavior of the final plot object
• The deseqresult2tbl() and deseqresult2DEgenes() are now replaced by the more flexible mosdef::deresult_to_df()
• The internally defined createLinkENS(), createLinkGeneSymbol(), and createLinkGO() are now replaced by the equivalent functions in mosdef
• The Roxygen-based documentation now supports markdown. No visible changes should appear to the user, as the content should have stayed fairly the same
• Although no visible changes for the end user are expected, the incoming major version bump will reflect the change in the dependency graph, ensuring that this is noticed at least at the version numbering level

GeneTonic 2.8.0

Other notes

• Updated functions used from other packages to reflect changes in their API/nomenclature
• Adapted the internal code of functions to the latest version of igraph - no changes happening for the end user

GeneTonic 2.6.0

Bug fixes

• describe_gtl() correctly extracts the number of up and down regulated genes from the DE results
• Fortified the behavior of gs_scores() to handle cases where only one gene would be included in the signature to plot

GeneTonic 2.4.0

New features

• enhance_table() has now the possibility to plot the visual summaries as ridge lines.
• When plotting the gene expression for the selected features in the gene-geneset-graph box, it is now possible to disable the labels from being displayed (could lead to unnecessary clutter sometimes).

Other notes

• Fortified the behavior of gene_plot() to fail early when providing an invalid value to the intgroup parameter.

GeneTonic 2.2.0

New features

• gs_heatmap gains the winsorize_threshold parameter, to control the behavior of the geneset heatmap in presence of extreme values, either negative or positive ones. If not specified, the heatmap is not introducing any winsorization.
• map2color() has a behavior that better accounts for asymmetric ranges of values. This propagates to some of the functions that use it for mapping to colors, such as enrichment_map(), or ggs_backbone().

Other notes

• Fixed the behavior of the reactive elements after uploading the GeneTonicList object at runtime.
• Fixed the label namings for the gs_heatmap function
• The enhance_table() function can handle the case where a gene is in the enrichment results table but not present in the annotation (e.g. annotations are updated, so some correspondences might get lost). It also presents an informative message on which genesets/genes are potentially responsible for the behavior.
• Some additional checks are in place for controlling the cases where the z_score of a geneset is detected as NA (e.g. because there was a mismatch between gene names and identifiers in the annotation).

GeneTonic 2.0.0

New features

• GeneTonic now offers the possibility to upload a GeneTonicList at runtime. This makes it possible to use the app as a server-like dashboard, which runs by default on no dataset provided, and populates its components upon successfully providing the data as expected
• The GeneSpector functionality in the Welcome panel provides a means to explore any gene in the expression set, coloring and grouping by any experimental covariate of interest
• It is possible to enter a set of genes and genesets in the Bookmarks panel, and these can be doubled checked against the available features of the current GeneTonicList - this, combined to the upload functionality, makes it possible to easily compare different gtl objects
• The GeneTonic app has a button to export the currently provided dataset - regardless of the input format - as a GeneTonicList. This is especially useful if one is providing the individual components (dds, res_de, res_enrich, annotation_obj) and would like to obtain the correct serialized object
• gs_upset adds the possibility to represent the results of enrichment analyses as upset plots, with the option to decorate them with DE-related information

Other notes

• The manuscript about GeneTonic is now published on BMC Bioinformatics at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04461-5 - the citation item has been updated accordingly
• The jittered position in the gene_plot is now completely reproducible, by setting a seed internally in the jitter generating function

GeneTonic 1.6.0

New features

• GeneTonic can now accept the input of clusterProfiler's gene set enrichment analysis functions (gseGO and GSEA), as implemented in the shake_gsenrichResult() function
• Below each plot and interactive widget, we provide a button that opens up a modal window where the code required to reproduce that output is shown as a snippet. These can be readily copied in extended reports or used to document the exploratory process.

Other notes

• The manuscript about GeneTonic is now available on bioRxiv at https://www.biorxiv.org/content/10.1101/2021.05.19.444862v1 - the citation item has been updated accordingly
• GeneTonic's Shiny app now uses the latest version of bs4Dash, which introduced some breaking changes. Most elements should be now available as they were in the original implementation

GeneTonic 1.4.0

New features

• The main function GeneTonic() gains an extra parameter, gtl - this can be used to provided a named list object where a single parameter is passed (e.g. after loading in a single serialized object), while the functionality stays unaltered. The same gtl parameter is also exposed in other functions of the package - see the vignette for some examples, or check the documentation of each specific function. To create this object in a standardized manner, the function GeneTonic_list() is now available.

• A new function to perform fuzzy clustering (following the implementation of DAVID) is added - see gs_fuzzyclustering(). It returns a table with additional information on the cluster of genesets and the status of each set in the group.

• The ggs_backbone() function can extract the bipartite graph backbone from the Gene-Geneset graph, this can be further explored below the main element in the Gene-Geneset panel. Once the backbone is created, you are one step away from checking out the genes that act as "hubs" in the Gene-Geneset graph, and possibly identify the nodes playing an essential role based on their connectivity.

• A new function, signature_volcano(), adds a signature volcano plot to the Gene-Geneset panel. This plot displays the genes of a chosen geneset in color, while the remaining genes of the data are shown as shaded dots in the background. The color and transparency of the displayed genes can be chosen by the user, as well as the option to display the gene names of all genes in the geneset.

• gs_summary_overview() can also generate bar plots instead of the default segment-dot (lollipop) plots.

• A new function, summarize_ggs_hubgenes(), builds a DT datatable for the Gene-Geneset panel. This table lists the individual genes of the input data and their respective degree in the Gene-Geneset graph. Furthermore, action buttons linking to the NCBI, GeneCards and GTEx databases are included for each gene.

• gene_plot() gains the extra labels_display argument to control whether the labels are at all shown; now the display of the labels is also respecting the jitter of the points

Other notes

• gs_heatmap() has now the possibility to set the arguments to the call to heatmap generating function, via ellipsis
• gs_heatmap() handles the colors in a consistent way over the different executions, without relying on the random palettes provided by the Heatmap's annotation functionality - could have been misleading if encountering too similar hues are randomly picked
• the plots obtained via gs_mds() and gs_volcano() now always display the line segments for the data points to be labeled (increasing the readability - as "matching back the label to the drawn circle" - thanks for the suggestion!)

GeneTonic 1.2.0

New features

• The geneset distillery is officially open! GeneTonic offers functionality to aggregate together gene sets into overarching biological themes, based on a network-based refinement of the enrichment map. Corresponding graphical functionalities are also extended to accommodate meta-genesets. An efficient implementation for the Markov clustering on graph objects is also provided

• GeneTonic can now receive the input of many other tools for functional enrichment analysis - this includes the output (text export) of DAVID (shake_davidResult), enrichr (from website and via the package, with shake_enrichrResult), fgsea (shake_fgseaResult), and g:Profiler (with shake_gprofilerResult, which can handle the textual output from the website, as well the one from the call to the gost in gprofiler2)

• An export button to a SummarizedExperiment object for iSEE and its underlying machinery has been added. If the visualization options in GeneTonic are not exactly what you would expect, you might find an excellent venue in the iSEE framework

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.
• gs_heatmap has a new parameter, plot_title, to override the title to be displayed and set it to any custom string
• It is now possible to save a snapshot of the graphs created with visNetwork
• The Gene Box now also contains links to the GTEx portal for the selected feature
• export_to_sif enables to export a graph object to a text file, encoded with the SIF format

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 datatables 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!

federicomarini/GeneTonic documentation built on Oct. 10, 2024, 8:49 p.m.