Changelog

Source: NEWS.md

ideal 1.99.0

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

ideal 1.18.0

Bug fixes

  • Fixed the unexpected behaviour when decorating the signature heatmap with colData elements

Other notes

  • Some alignments of the UI elements in the ideal() app, to harmonize the content of the page
  • Updated the icons in the user interface to match recent changes in the names from FontAwesome

ideal 1.16.0

New features

  • It is now possible to export the processed data (count data, results, functional enrichment table) into a combined list object, which can be seamlessly fed into GeneTonic (http://bioconductor.org/packages/release/bioc/html/GeneTonic.html).
  • Adjusted the behavior for the modeling with LRT, with extra notifications to inform the user on how to make the most out of the functionality.

Other notes

  • The manuscript of ideal is now published in BMC Bioinformatics! The citation file has been updated accordingly.
  • A full round of styler has been applied to the codebase.

ideal 1.14.0

Other notes

  • Replaced dependency from d3heatmap with the functionality of heatmaply
  • Additional notifications are returned when closing the app while saving the state to the R environment - both in the console as a message, and in the UI via showNotification
  • The vignette and the tour contain a section about the format required to run ideal correctly
  • The vignette also indicates some exemplary steps after exporting the values to the R environment, showcasing how to perform additional functional enrichment analyses e.g. via fgsea or gprofiler2

ideal 1.12.0

New features

  • Implemented a series of gentle fail mechanisms to avoid abrupt crashing of the app if the expected objects or formats are not provided

Other notes

  • Alignments of UI elements have been adjusted
  • Updated citation info - the preprint for ideal, “ideal: an R/Bioconductor package for Interactive Differential Expression Analysis”, is now published at bioRxiv, https://doi.org/10.1101/2020.01.10.901652
  • Data transformation (for table viewing and visualizations, where homoscedastic data is expected) is now taken care of with the variance stabilizing transformation (vst), instead of the rlog
  • The installation information in the README.md includes a troubleshooting section to solve some common issues one might encounter
  • Added a collapsible element in the Data Setup panel, to remind users to perform proper Exploratory Data Analysis (e.g. with pcaExplorer) before testing for Differential Expression

ideal 1.10.0

New features

  • ggplotCounts gains a new parameter, labels_repel, to control the placement of the different labels in the plot - this can be useful when a large number of samples is available

Bug fixes

  • Fixed an error in the initialization of the app due to a new behavior introduced by shinyAce in version >= 0.4.0 - occurred in the same way as for pcaExplorer

Other notes

  • Better class checks via is(...) as per BiocCheck suggestion

ideal 1.8.0

New features

  • plot_ma gains an additional parameter, labels_repel, for better placing the labels on the features to mark
  • The pairwise correlation plots can now use logarithmic scale in the axes, use smaller subsets of the data for quicker inspection, and resizes the correlation info proportionally to its intensity
  • The id types can now be chosen among the keytypes of the corresponding annotation packages (which still need to be installed when ideal is launched). Other input fields that specify id types also behave in a similar manner (e.g. in the Signature Explorer tab). This caused a problem for scenarios where common id types such as ENSEMBL are not available, like in Arabidopsis (where ids are provided often as TAIR) - thanks to Marc Galland for picking this up in https://github.com/federicomarini/ideal/issues/1
  • The Signatures Explorer tab also has a fully fledged tour for first-time users, together with a collapsible help panel to describe its functionality in brief
  • The zoomed MA-plot gains a new widget to control the labels size for the names of the genes
  • It is possible to export the input data together with the results in a combined SummarizedExperiment object, which can be seamlessly fed into iSEE (http://bioconductor.org/packages/release/bioc/html/iSEE.html). This leverages a new function, wrapup_for_iSEE, which is available and exported from ideal.

Other notes

  • An information box has been added to provide detailed information on the required input formats
  • Added notification to specify how to install the airway package for demonstration purposes if not already available
  • The Signatures Explorer tab is now displayed in a conditional panel, i.e. only when the required inputs are provided

ideal 1.6.0

New features

  • Added extra diagnostic to results exploration (stratified pvalues histograms, schweder-spjotvoll plot)
  • Added functionality for the tab Signatures Explorer: read in gmt files, and explore signatures for all/DE genes visually as heatmaps. The signatures can also be provided in the main call of the function as an argument, on top of uploading at runtime
  • Different handling of the selection of ids/gene names, now not requiring anymore that the result is computed, but based on the dds object (and on the presence or not of the annotation object)

Other notes

  • Built project website via pkgdown, with customized reference structure
  • Added a NEWS.md file to track changes to the package
  • Updated the report template as well for including new functionality, and also updated vignette entry
  • Correctly adding the resources to shinyBS, loaded via .onLoad
  • Replaced the first tour structure and call
  • New skin for the app, also with logo in the title header
  • Instructions start collapsed for more compact main page
  • Edited link in button to provide feedback, with subject specified

Bug fixes

  • Fixed behavior of rendering inline the content of the report - did not work properly for server deployed instances

ideal 1.4.0

New features

  • Specified single go term selection for generating heatmaps of gene signatures
  • Added support for logFC shrinkage, following the latest devels of DESeq2

Bug fixes

  • Corrected output for the vignette, as html_document2 is now deprecated
  • Menus are back in the expanded form
  • Fixed the behavior with addMLE

Other notes

  • Added further progress indicators to give feedback during lengthy steps
  • Improved ggplotCounts for better scale display, using exact arg matching, defaulting to the transformed counts

ideal 0.99.0

New features

  • Ready for Bioc submission
  • Completed the news

ideal 0.9.1

New features

  • Added Instructions fully from rendered version of the vignette to have available at runtime
  • Added support for downloading all plots and tables

ideal 0.9.0

New features

  • Interactive tours are covering now all tabs, with extensive walkthroughs for the user
  • Added all screenshots to vignette

ideal 0.6.2

New features

  • Interactive tours are now available, coded in external files
  • Travis-CI is now supported

ideal 0.6.0

New features

  • Added MA plot with extra custom list to avoid manual selection of many genes
  • MA plot function now automatically supports subset of gene to be extra plotted
  • Added documentation with roxygen to all functions
  • Heatmap functions for genes annotated to a GO term as signature
  • Template report also provided
  • Full draft of vignette now available, working towards bioc submission
  • Added textual help to all sections, with collapsible element
  • Added proof of principle to have interactive tours based on rintrojs

ideal 0.4.0

New features

  • Gene box info added, based on rentrez
  • New look for MA plots and volcano plots

ideal 0.3.0

New features

  • Restructuring of the folders done, package can be correctly installed, loaded - namespace, description are set up

ideal 0.2.0

New features

  • Correct structure of the package

ideal 0.1.0

New features

  • Package created!