@@ -287,18 +287,18 @@ The `GeneTonic` app is built with `r BiocStyle::CRANpkg("shiny")`, and its layou

 The dashboard navbar (as it is called in `bs4Dash`) contains two dropdown menus, which can be expanded by clicking on the respective icons (<i class="fa fa-book"></i> and <i class="fa fa-info"></i>).

 These provide additional buttons to do one the following:

-- <i class="fa fa-book"></i> inspect the `r BiocStyle::Biocpkg("GeneTonic")` vignette (either the one installed in bundle with the package, or the online version)

-- <i class="fa fa-question-circle"></i> read some first help information on `GeneTonic` (What the package does in brief, what is required to run properly)

-- <i class="fa fa-info-circle"></i> display information about the current session (via `sessionInfo()`)

-- <i class="fa fa-heart"></i> show some general information on `r BiocStyle::Biocpkg("GeneTonic")`, like where to find its development version (and contribute to that), or how to cite this tool.

+- <i class="fa fa-book"></i> - inspect the `r BiocStyle::Biocpkg("GeneTonic")` vignette (either the one installed in bundle with the package, or the online version)

+- <i class="fa fa-question-circle"></i> - read some first help information on `GeneTonic` (what the package does in brief, what is required to run properly)

+- <i class="fa fa-info-circle"></i> - display information about the current session (via `sessionInfo()`)

+- <i class="fa fa-heart"></i> - show some general information on `r BiocStyle::Biocpkg("GeneTonic")`, like where to find its development version (and contribute to that), or how to cite this tool.

-Additionally, one fundamental button is present in the navbar: `r shiny::actionButton("bookmarker", label = "Bookmark", icon = shiny::icon("heart"), style = "color: #ffffff; background-color: #ac0000; border-color: #ffffff", class = "ml-5")`.

+Additionally, one fundamental button is present in the navbar - labeled "Bookmark", with the heart <i class="fa fa-heart"></i> icon.

 This serves the purpose of bookmarking genes and gene sets of interest while exploring your data in an interactive session.

-This functionality will be exploited in the <i class="fa fa-bookmark"></i> section of the app, where a complete HTML report can be generated as a reproducible artifact.

+This functionality will be exploited in the <i class="fa fa-bookmark"></i> Bookmarks section of the app, where a complete HTML report can be generated as a reproducible artifact.

 ## Sidebar

-On the left side of the app, by clicking on the <i class="fa fa-bars"></i> icon (or if the app is viewed in full screen, by simply moving the mouse over to the left side), the sidebar menu is triggered.

+On the left side of the app, by clicking on the <i class="fa fa-bars"></i> menu bar icon (or if the app is viewed in full screen, by simply moving the mouse over to the left side), the sidebar menu is triggered.

 This constitutes the main way to access the different tabs of `GeneTonic()`, which will be explained in more detail in the next section (\@ref(functionality)).

 ## Controlbar

@@ -310,7 +310,7 @@ There you can find widgets that control the appearance of output (plots, tables,

 The main body of the `GeneTonic` application is structured in tabs that are activated by clicking on the respective icons or text in the sidebar.

-While the Welcome tab might be self-explanatory, the functionality of each tab can go in depth, and new users can benefit of the `r shiny::actionButton("tour", label = "", icon = shiny::icon("question-circle"), style = "color: #0092AC; background-color: #FFFFFF; border-color: #ffffff")` button to trigger an interactive tour of `GeneTonic`, which allows users to learn the basic usage mechanisms by doing.

+While the Welcome tab might be self-explanatory, the functionality of each tab can go in depth, and new users can benefit of the question circle button (<i class="fa fa-question-circle"></i>) button to trigger an interactive tour of `GeneTonic`, which allows users to learn the basic usage mechanisms by doing.

 During a tour, the highlighted elements respond to the user's actions, while the rest of the UI is kept shaded.

 Tours can be interrupted anytime by clicking outside of the focused window, and arrows (left, right) can be used as well to navigate between steps.

 The tour functionality is provided by the beautiful `r BiocStyle::CRANpkg("rintrojs")` package.

@@ -350,7 +350,7 @@ The interactivity in this graph is essential for zooming, panning, and selecting

 The node selection, in particular, triggers a drill-down exploration, which populates a box on the right side, either with a signature heatmap (for a gene set), or with an expression plot, split by the experimental covariates of interest (for a gene) - this behavior can be controlled by the "Group/color by" selectize widget in the control sidebar.

 In both cases, some HTML content is also generated, with buttons linking to external databases where to retrieve additional information (e.g. ENSEMBL, NCBI, AmiGO, ...).

-A demonstration of how to use this panel effectively is provided by the tour, triggered by clicking on the `r shiny::actionButton("tour", label = "", icon = shiny::icon("question-circle"), style = "color: #0092AC; background-color: #FFFFFF; border-color: #ffffff")` button in the upper right corner of the tab.

+A demonstration of how to use this panel effectively is provided by the tour, triggered by clicking on the question circle button (<i class="fa fa-question-circle"></i>) button in the upper right corner of the tab.

 **Bookmarking from the Gene-Geneset panel:** When clicking on the Bookmark button while in this tab, it is possible to add to the shortlisted items of interest both genes and gene sets.

 To do so, while one of the nodes is selected, click on the button with the mouse - or alternatively, click on the Left Ctrl button of your keyboard.

@@ -370,7 +370,7 @@ The `z_score` and `aggr_score` (in the simplest form, a mean of the log2FoldChan

 The interactive flavor in this tab permits a quick exploration of the signature heatmaps for the genesets of interest by simply clicking on a node; this also triggers the display of some HTML content, if related to a Gene Ontology term.

-A demonstration of how to use this panel effectively is provided by the tour, triggered by clicking on the `r shiny::actionButton("tour", label = "", icon = shiny::icon("question-circle"), style = "color: #0092AC; background-color: #FFFFFF; border-color: #ffffff")` button in the upper right corner of the tab.

+A demonstration of how to use this panel effectively is provided by the tour, triggered by clicking on the question circle button (<i class="fa fa-question-circle"></i>) button in the upper right corner of the tab.

 In the section below the interactive enrichment map, the functionality for the _distillation_ of gene sets into meta-genesets is provided.  

 In brief, a community detection algorithm is run on the graph underlying the enrichment map, and the additional information extracted is rendered as a table, linked to a meta-geneset box to display the expression signature for all its member genes.

@@ -387,7 +387,7 @@ We avoid (re)rendering all plots at once by placing them as content of different

 Interactive versions of the plots are returned via calls to `ggplotly`.

-A demonstration of how to use this panel effectively is provided by the tour, triggered by clicking on the `r shiny::actionButton("tour", label = "", icon = shiny::icon("question-circle"), style = "color: #0092AC; background-color: #FFFFFF; border-color: #ffffff")` button in the upper right corner of the tab.

+A demonstration of how to use this panel effectively is provided by the tour, triggered by clicking on the question circle button (<i class="fa fa-question-circle"></i>) button in the upper right corner of the tab.

 ## The GSViz panel

@@ -403,7 +403,7 @@ This includes, for example:

 As in many other panels, the control over the number of genesets displayed is tweaked with the widget in the right sidebar, "Number of genesets".

-A demonstration of how to use this panel effectively is provided by the tour, triggered by clicking on the `r shiny::actionButton("tour", label = "", icon = shiny::icon("question-circle"), style = "color: #0092AC; background-color: #FFFFFF; border-color: #ffffff")` button in the upper right corner of the tab.

+A demonstration of how to use this panel effectively is provided by the tour, triggered by clicking on the question circle button (<i class="fa fa-question-circle"></i>) button in the upper right corner of the tab.

 ## The Bookmarks panel

@@ -435,7 +435,7 @@ This report will serve as a useful means to generate a permanent and reproducibl

 Ideally, each live session with `GeneTonic` could terminate with a call to `happy_hour()` - admittedly, an aperitivo should start with that, and not end - please accept our apologies :) .

-A demonstration of how to use this panel effectively is provided by the tour, triggered by clicking on the `r shiny::actionButton("tour", label = "", icon = shiny::icon("question-circle"), style = "color: #0092AC; background-color: #FFFFFF; border-color: #ffffff")` button in the upper right corner of the tab.

+A demonstration of how to use this panel effectively is provided by the tour, triggered by clicking on the question circle button (<i class="fa fa-question-circle"></i>) button in the upper right corner of the tab.

 In this panel, an export button to a `SummarizedExperiment` object to be provided as input to the `r BiocStyle::Biocpkg("iSEE")` package has been added in version >= 1.2.0. 

 This enables further and fine-grained visualization options in the `iSEE` framework -  if the flavors of `GeneTonic` are not yet what you would want, you might find an excellent venue there.