NEWS

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scOverlay 0.99.5

Initial Bioconductor submission

• Introduced plotOverlay() for displaying a foreground feature over a contextual background in a two-dimensional SingleCellExperiment embedding. Background and foreground layers have independent colour scales and can represent gene expression, cell metadata, or a solid colour.
• Added foreground-only cell selection, preserving the full embedding as background context. Supports configurable assays, point sizes, transparency, colour limits, legends, and drawing order.
• Added plotGeneOverlay() for plotting one or more gene-expression overlays.
• Added plotOverlayPerGroup() and plotOverlayPerNestedGroup() for comparing subsets across grouped panels, with optional shared foreground scales and legends. Nested layouts support automatic selection between compact and aligned grids, with informative panel titles.
• Added bivariate foreground colouring for two numeric features, with plotBivariateLegend() for the corresponding two-dimensional legend.
• Added combination colouring for the thresholded positive/negative patterns of two to five numeric features.
• Added palette utilities getPalette(), listPalettes(), and plotPalettes() for selecting, inspecting, and previewing categorical, continuous, and bivariate colour palettes.
• Added optional point rasterization for dense embeddings while retaining ggplot2-compatible plot output.