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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:
bg_alpha = 0.25 by default, making them more visually
recessive.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.grDevices::adjustcolor,
graphics::*, stats::cov,
stats::loess, stats::predict; removed
spatstat.explore::envelope (no longer needed).grDevices,
graphics, stats.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.
>= 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).testthat unit tests covering all exported
functions."tlsR-workflow" demonstrating the full
analysis pipeline.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.