NEWS

teal.modules.hermes 0.2.0

Added teal.logger functionality for logging changes in shiny inputs in all modules.
Introduce transformators parameter in modules.

Added placeholders for assaySpec, adtteSpec and geneSpec inputs when no option is selected.
Disabled the select input for assaySpec and adtteSpec when there are no options available.
For module developers: The module gets teal_data object in the UI and reactive(<teal_data>) in the server

Updated the documentation and vignettes with the new way of specifying data for teal::init(). The data argument accepts teal_data object.

Filtering data with the filter panel now correctly triggers the sampleVarSpecModule.

Replaced datasets argument containing FilteredData with the new arguments data (tdata object) and filter_panel_api (FilterPanelAPI).

Improve the selection of sample variables in the forest module (tm_g_forest_tte) such that only categorical variables can be selected in the first place.

Added a template to the pkgdown site.
Updated package authors.
Added the option categorical_only to the sampleVarSpec server module, which allows to only show categorical sample variables for selection.

Rewrote modules to use moduleServer and updated call to plot_with_settings_srv after changes in teal.devel.
Replaced calls to teal::root_modules with teal::modules following deprecation of teal::root_modules.
Added basic logging to the modules.
Fixed the geneSpecInput so that the hermes app doesn't fail anymore (on chrome) on an experiment with no genes.

Updated legend for the PCA plot.
Gene selection with more than a few thousand genes no longer hangs the application. This is achieved through a different selection input in the corresponding geneSpec shiny module.
Only atomic columns of colData with at least one value can now be selected in the sampleVarSpecModule.

Updated R version requirement to >= 3.6.
Updated sampleVarSpec and geneSpec modules with new icons to remove warnings when using shiny version >= 1.7.
Removed dependencies on deprecated packages utils.nest and test.nest.

First release of the teal.modules.hermes package, which contains teal modules for RNA-seq analysis using the hermes package.
New users should first begin by reading the README.md of the teal.modules.hermes package to become familiar.

tm_g_barplot is a barplot module for RNA-seq gene expression analysis.
tm_g_boxplot is a boxplot module for RNA-seq gene expression analysis.
tm_g_forest_tte is a survival forest plot module to analyze RNA-seq gene expression data together with survival data.
tm_g_km is a Kaplan-Meier plot module to analyze RNA-seq gene expression data together with survival data.
tm_g_pca is a principal components analysis plot module for RNA-seq gene expression analysis.
tm_g_quality is a quality control module for RNA-seq gene expression data.
tm_g_scatterplot is a scatterplot module for RNA-seq gene expression analysis.
tm_g_volcanoplot is a differential gene expression analysis module.