Extra docs vignette markdownboard (#116)

* adding documentation for two additional panels - already in the codebase, just not highlighted yet in the vignette

* adding screenshots, created via appshot on the app objects

* newer roxygen version

* manpage re-created

* udpated news

* version bump, 1.15.1

* updating GHA to use latest Bioc devel version

.github/workflows/check-bioc.yml

@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.17', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: '3.17'}
-          - { os: windows-latest, r: 'devel', bioc: '3.17'}
+          - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: 'devel'}
+          - { os: windows-latest, r: 'devel', bioc: 'devel'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: iSEEu
 Type: Package
 Title: iSEE Universe
-Version: 1.15.0
-Date: 2023-03-10
+Version: 1.15.1
+Date: 2024-03-07
 Authors@R: 
     c(
     person("Kevin", 
@@ -73,6 +73,6 @@ BugReports: https://github.com/iSEE/iSEEu/issues
 biocViews: ImmunoOncology, Visualization, GUI, DimensionReduction, 
     FeatureExtraction, Clustering, Transcription, 
     GeneExpression, Transcriptomics, SingleCell, CellBasedAssays
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr

NEWS.md

@@ -1,3 +1,8 @@
+# iSEEu 1.15.1
+
+* Expanded the content of the vignette, to have `AggregatedDotPlot()` and
+the `MarkdownBoard()` panels highlighted
+
 # iSEEu 1.11.2
 
 * Adjusted code to correctly parse and rename KEGG pathway identifiers.

vignettes/iSEEu.Rmd

@@ -258,6 +258,71 @@ This is useful for applying sequential restrictions on the data, equivalent to g
 -  `modeReducedDim()` will launch an app with multiple reduced dimension plots.
 This is useful for examining different views of large high-dimensional datasets (e.g., single-cell studies).
 
+# Miscellaneous panels
+
+`r Biocpkg("iSEEu")` also includes a number of other panel types, that one can find useful within different contexts.
+
+Coupled to each chunk of code listed below, it is possible to display a screenshot of the app showcasing them.
+
+**AggregatedDotPlot**
+
+```{r}
+app <- iSEE(
+    sce,
+    initial = list(
+        AggregatedDotPlot(
+            ColumnDataLabel="Primary.Type",
+            CustomRowsText = "Rorb\nSnap25\nFoxp2",
+            PanelHeight = 500L, 
+            PanelWidth = 8L
+        )  
+    )
+)
+
+## To be later run as...
+# app
+## ... or
+# shiny::runApp(app)
+```
+
+```{r, echo=FALSE}
+SCREENSHOT("screenshots/aggrodotplot.png", delay=30)
+```
+
+This can be very useful as an alternative to the `ComplexHeatmapPlot` panel, as sometimes it is not just about the shifts in average expression levels, but true biological signal can be found e.g. in scenarios such as differential detection.
+
+**MarkdownBoard**
+
+The `MarkdownBoard` panel class renders Markdown notes, user-supplied, into HTML to display inside the app. 
+
+```{r}
+app <- iSEE(
+    sce, 
+    initial = list(
+        MarkdownBoard(
+            Content = "# `iSEE` notepad\n\nYou can enter anything here.\n\nA list of marker genes you might be interested into:\n\n- Snap25\n- Rorb\n- Foxp2\n\nThis makes it easier to copy-paste while staying inside `iSEE`.  \nAs you can notice, the full power of markdown is at your service.\n\nHave fun exploring your data, in an even more efficient manner!\n", 
+            PanelWidth = 8L,
+            DataBoxOpen = TRUE
+        )
+    )
+)
+
+## To be later run as...
+# app
+## ... or
+# shiny::runApp(app)
+```
+
+This is useful for displaying information alongside other panels, or for users to simply jot down their own notes (and re-use them more efficiently later).
+
+```{r, echo=FALSE}
+SCREENSHOT("screenshots/markdownboard.png", delay=30)
+```
+
+The content of the `MarkdownBoard` is included in the `Data parameters` portion of the panel, as visible in the screenshot.
+
+`r Biocpkg("iSEE")` will take care of rendering your notes into good-looking yet simple HTML, that can embedded in a variety of analytic workflows for the data under inspection.
+
 # Contributing to `r Biocpkg("iSEEu")`
 
 If you want to contribute to the development of the `r Biocpkg("iSEEu")` package, here is a quick step-by-step guide: