Changelog • tlsR

tlsR 0.3.0

scan_clustering() — completely redesigned. The function no longer runs Monte Carlo CSR envelope tests. Instead it computes the K-integral clustering index (mean positive L excess over theoretical CSR) in each sliding window and — when plot = TRUE (now the default) — draws a spatial base-graphics map with LOESS-smoothed L-excess curves and numeric CI labels overlaid inside each qualifying window. The returned value is a plain list of Lest objects (one per qualifying window). The nsim argument has been removed; a new min_phen_cells argument controls the per-window phenotype-cell threshold.

calc_icat() — fixed sign-ambiguity bug. The previous implementation returned the raw signed trace of the FastICA mixing matrix, which could be negative. The index is now computed as 100 * sqrt(v1 + v2 + 2*sqrt(v1*v2)) / nrow(X) — a normalised trace-standard-deviation of the ICA-reconstructed coordinates — which is always non-negative and reflects average spatial spread per cell in microns.
plot_TLS() — two visual improvements:
- Background (non-TLS, non-TIC) cells are now rendered with bg_alpha = 0.25 by default, making them more visually recessive.
- TIC cells are drawn at point_size * tic_size_mult (default 1.8x), making them slightly larger than TLS cells. Both new arguments (bg_alpha, tic_size_mult) are fully exposed.

NAMESPACE updated: added grDevices::adjustcolor, graphics::*, stats::cov, stats::loess, stats::predict; removed spatstat.explore::envelope (no longer needed).
DESCRIPTION Imports extended to declare grDevices, graphics, stats.
Vignette updated throughout to reflect all changes.

CRAN release: 2026-04-09

summarize_TLS() — produces a tidy data.frame with one row per sample summarising detected TLS count, size, cell fractions, T-cell clusters, and (optionally) per-TLS ICAT scores.
plot_TLS() — ggplot2-based spatial scatter plot of TLS and T-cell cluster membership, using a colourblind-friendly palette. Returns the ggplot object invisibly for further customisation.

calc_icat() — now returns NA_real_ with an informative message() when a TLS has fewer than 3 cells or when FastICA fails to converge, instead of throwing an error.
detect_tic() — now returns the updated ldata list visibly (was invisible). Two new arguments min_pts and min_cluster_size expose HDBSCAN tuning parameters that were previously hard-coded. Non-T-cell rows now receive NA (not 0) in the tcell_cluster_hdbscan column.
scan_clustering() — the return value is now a named list of result objects each containing Lest, envelope, window_center, and n_cells. New nsim and min_cells arguments added. Tissue-extent guard now fires before seq() is called, preventing a wrong-sign error on small datasets.
All functions — phenotype matching now accepts both singular ("B cell", "T cell") and plural ("B cells", "T cells") labels via internal helpers .is_bcell() and .is_tcell().
All functions — the global ldata fallback now emits a warning() asking users to pass ldata explicitly. This behaviour is deprecated and will be removed in v0.3.0.

plot_TLS() — replaced the Greek mu character (\u03bc) in axis labels with plain ASCII "um" to prevent encoding failures on systems with limited locale support.
plot_TLS() — now returns the ggplot object truly invisibly (no implicit print() call), preventing spurious rendering during R CMD check.

Minimum R version raised to >= 4.0.0.
spatstat imports updated to spatstat.geom and spatstat.explore.
VignetteBuilder: knitr added to DESCRIPTION (was missing, causing a vignette WARNING in R CMD check).
LICENSE.md and cran-comments.md added to .Rbuildignore (were generating a NOTE about non-standard top-level files).
Comprehensive testthat unit tests covering all exported functions.
Vignette "tlsR-workflow" demonstrating the full analysis pipeline.

CRAN release: 2025-12-18