diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 0cc771c..b54ab26 100644 --- a/.github/workflows/check-bioc.yml +++ b/.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: diff --git a/DESCRIPTION b/DESCRIPTION index 9c8f5cc..5aba99d 100644 --- a/DESCRIPTION +++ b/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 diff --git a/NEWS.md b/NEWS.md index 7c64fba..9b214f0 100644 --- a/NEWS.md +++ b/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. diff --git a/man/iSEEu-pkg.Rd b/man/iSEEu-pkg.Rd index 9276ae4..b931f83 100644 --- a/man/iSEEu-pkg.Rd +++ b/man/iSEEu-pkg.Rd @@ -4,6 +4,7 @@ \name{iSEEu-pkg} \alias{iSEEu} \alias{iSEEu-package} +\alias{iSEEu-pkg} \title{iSEEu: iSEE Universe} \description{ \code{iSEEu} is a package that provides modes and panels for \code{iSEE}, allowing easy configuration of \code{iSEE} applications. diff --git a/vignettes/iSEEu.Rmd b/vignettes/iSEEu.Rmd index d1c6171..8b850bf 100644 --- a/vignettes/iSEEu.Rmd +++ b/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: diff --git a/vignettes/screenshots/aggrodotplot.png b/vignettes/screenshots/aggrodotplot.png new file mode 100644 index 0000000..09538ef Binary files /dev/null and b/vignettes/screenshots/aggrodotplot.png differ diff --git a/vignettes/screenshots/markdownboard.png b/vignettes/screenshots/markdownboard.png new file mode 100644 index 0000000..975d079 Binary files /dev/null and b/vignettes/screenshots/markdownboard.png differ