NEWS

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SummarizedHeatmap 0.99.0

• Initial Bioconductor development release.
• Introduces the SummarizedExperiment-derived heatmap representation, explicit clustering helpers, composable ggplot2 components, and patchwork assembly.
• assay<-/assays<- on a SummarizedHeatmap now invalidate stale cluster-derived state: a stored row/column dendrogram is cleared and that axis's order reset to natural order, while axes without a stored dendrogram (e.g. a manual order) are left untouched. Assay replacement never reclusters automatically.
• SummarizedHeatmap() now preserves the original assay name when constructing from a SummarizedExperiment, instead of always renaming it to "matrix". An explicit assay argument is now validated even for a single-assay SummarizedExperiment, rather than being silently ignored.
• plotHeatmap(collectGuides = FALSE) no longer reserves an empty guide-area column: the guide_area() panel and its guideWidth column are now omitted from the layout entirely instead of being left blank.
• The SummarizedHeatmap validity method now requires the sole assay to be a numeric, non-complex matrix, matching the constructor's own check. This means assay<-/assays<- reject replacements that would leave a non-numeric, complex, or non-matrix assay.
• plotRowData()'s and plotColData()'s side argument now names where the variable-name axis text is anchored, instead of (for plotColData(), a no-op) which side of the heatmap the panel sits on: plotRowData(side =) now takes "top"/"bottom" (the narrow axis the label sits on) and plotColData(side =) now takes "left"/"right". plotHeatmap()'s rowAnnotationSide/colAnnotationSide arguments are unchanged and still control panel placement only.
• The vignette now demonstrates manual column ordering via SummarizedHeatmap(colOrder = ).