NEWS
panoramic 0.99.3
- Major workflow/API restructuring:
- Added
panoramic_analyze() as the canonical end-to-end workflow.
panoramic() now delegates to panoramic_analyze() and returns a unified
list with prep, stats, pooled, and tables.
- Removed legacy compatibility arguments from the main wrappers
(
meta_model, tau2, group_method, keep_boot).
- Replaced legacy two-stage group-comparison flow with multilevel modeling:
- Retired/unexported
panoramic_meta() and panoramic_compare_groups().
- Added/exported
panoramic_meta_mv() as the primary pooling API, including
single-stage two-group contrasts (beta_diff, se_diff, z_diff,
p_diff, fdr_diff) and optional group-specific heterogeneity estimates.
- Contrast direction is now deterministic for grouped analyses.
- Added new result access helpers:
panoramic_extract_contrast() for extracting spatialstats, meta, or
contrast tables.
- Pre-flattened tables are stored in
metadata(se)$panoramic$tables.
- Retired unused interpret/diagnostic helper prototypes
(
panoramic_sample_deviation(), panoramic_interpret_meta_mv()) from the
public API to reduce surface area.
- Expanded statistical and plotting functionality:
- Refactored
panoramic_spatialstats() internals for robustness (single-sample
support, clearer per-sample/pair failure handling, and optimized local
composition enrichment caching/bootstrapping).
- L-function variance is computed via a delta-method transform from
corresponding K-function estimates.
- Added
plot_representative_samples() and updated plot_volcano(),
plot_forest(), and network plotting helpers to align with multilevel
contrast outputs.
- Documentation/submission updates:
- Reworked vignette/tutorial to match the restructured workflow and current
plotting APIs.
- Added/updated man pages for newly exported functions and removed stale
legacy docs.
- Updated package metadata for Bioconductor review (
Depends: R (>= 4.6),
CITATION parsing fixes, .gitignore final newline).
- Review-driven hardening and consistency fixes:
panoramic_prepare() now performs explicit schema validation
(design$sample/design$group, duplicate sample IDs) and stronger
coordinate/window checks after filtering.
- Auto pair generation now uses observed marks (not unused factor levels),
preventing inflated impossible pair sets under
min_presence.
panoramic_meta_mv() now stops on ambiguous group labels after
sanitization (make.names) to avoid silent group collisions.
panoramic_spatialstats() now degrades to per-sample NA outputs when local
composition precompute fails, instead of aborting the full run.
create_spatial_network() now validates required rowData columns and
documents/guards nonstandard sig_operator = "gt" behavior.
- Plotting docs/messages now state the current two-group constraint
(
plot_forest(), plot_representative_samples()), and network man pages
are synced to current function signatures.
panoramic 0.99.0
- First Bioconductor submission of PANORAMIC.
- Added a full tutorial vignette showing how to prepare data, run pooled spatial analysis, and interpret results.
- Improved plotting functions for differential colocalization summaries.
- Added package citation metadata to make it easier to cite PANORAMIC and its associated preprint/release record.