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reglScatterplot 0.99.0

  • First Bioconductor submission.
  • Package restructured into one file per responsibility (utils.R, colors.R, scatterplot.R, sce.R, shiny.R).
  • Functions renamed to Bioconductor camelCase style: my_scatterplot() → reglScatterplot(), my_scatterplotOutput() / renderMy_scatterplot() → reglScatterplotOutput() / renderReglScatterplot(), enableMyScatterplotSync() → enableReglScatterplotSync(), updateMyScatterplotSize() → updateReglPointSize(), to_base64() → toBase64(). Argument naming has been harmonised to camelCase (group_var → groupBy, filter_vars → filterBy, size → pointSize, gene_names → pointLabels, center_zero → centerZero, filtered_indices → filteredIndices, selected_indices → selectedIndices, legend_title → legendTitle).
  • library() calls inside package code removed; explicit importFrom declarations added throughout.
  • Input validation added: coordinates, palettes, and filter arguments now fail fast with informative messages.
  • JavaScript widget bugs fixed:
    • empty ResizeObserver body now drives the public resize() so standalone HTML, RStudio Viewer and Jupyter outputs reflow correctly,
    • stale factory width / height references replaced with live container.getBoundingClientRect() measurements,
    • the previously undeclared prevNumPoints is now properly scoped,
    • CDN imports for d3 and regl-scatterplot are wrapped in try / catch and display a user-visible error when offline.
  • sizingPolicy() configured for the RStudio Viewer and Jupyter so rendering is correct outside Shiny.
  • Tests added under tests/testthat/ covering utilities, colour resolution and widget construction.
  • Vignette reglScatterplot.Rmd added, including a SingleCellExperiment walk-through.
  • DESCRIPTION updated for Bioconductor (biocViews, R >= 4.4.0, URL/BugReports, VignetteBuilder, Suggests for testing).
  • Auto-fit on resize: when the user has not yet panned/zoomed, container resize events re-run the data-aspect-preserving fit, eliminating the "bottom rows clipped" problem in Hyprland tiles, RStudio Viewer at non-default browser zoom, and flex/grid layouts that settle late.
  • Single-cell support: reglScatterplot(sce, x = "UMAP", colorBy = ...) pulls coordinates from reducedDim() and resolves colorBy against colData columns or feature rownames automatically. SpatialExperiment inputs use spatialCoords() when x = "spatial".
  • Z-channel quantisation (Uint16) cuts the standalone-HTML payload by another ~25% on top of the X/Y quantisation already in place. At 5M points the file drops from ~78 MB to ~39 MB.
  • New rangePadding argument (default 0.4) controls how much whitespace is added on each side of the data range. This is the recommended dial when clusters appear clipped at the edges of very small viewports - the previous fixed margin was not enough at narrow window sizes.
  • Known viewport behaviour: the widget renders inside its htmlwidgets container, which honours an explicit height = N pixel value verbatim. If the host window is shorter than N (e.g. a small browser tab, a tile in a tiling window manager), the bottom of the widget is clipped by the host viewport - not by reglScatterplot. Pass height = "100%" (or leave the argument out) to let the widget fill whatever vertical space is available.