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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Ran pkgdown::build_site() to regenerate docs/ from the current vignettes/ directory. Adds docs/articles/quickstart.html (with rendered plots) and removes the outdated basic_tutorial, TF_tutorial, and MPA_basics_microglia articles that were no longer backed by source .Rmd files.
- Add MacrostateTransitions and PlotMacrostateTransitions: coarse-grained group-level transition probability matrix with stability index heatmap - Add CombinePerturbAssays: additive delta superposition across perturbation assays - Fix PlotMacrostateTransitions matrix indexing bug (element-wise extraction) - New vignette: simulation_tutorial (full ModulePerturbation workflow + macrostate transitions + Markov chain analyses) - New vignette: advanced_NSCLC (step-by-step ApplyPerturbation / ApplyPropagation / PerturbationTransitions + CustomPerturbation + CombinePerturbAssays) - Update _pkgdown.yml with Advanced Use Cases article section - Update .gitignore to exclude macOS resource forks, vignette HTML build artifacts - Update CLAUDE.md: document module load GCC requirement for Rcpp compilation - Bump version to 0.1.0
…Attractors, update simulation vignette - Add R/MarkovPlots.R with PlotMarkovEmbedding (embedding colored by Markov score, centroid diamond overlays for source/sink, unconverged-cell greying, point ordering) and PlotMarkovScatter (cross-score scatter with adaptive color scaling) - Add rank_transform parameter to PredictAttractors for ECDF normalization of stationary distribution scores; sink detection always uses raw distribution - Update simulation_tutorial.Rmd: integrate new plot functions in Markov section, show raw vs ECDF attractor scores side-by-side, add binary attractor DimPlot with correct draw order, rename per-section plot vars and add 2x2 summary patchwork, wrap log2FC table in a collapsible dropdown, sentence-case all section headings - Add tests/testthat/test-MarkovPlots.R with 12 tests for both new functions - Update DESCRIPTION (add ggrepel to Imports) and NAMESPACE accordingly - Remove stale vignettes/simulation_tutorial.html; rebuild docs/articles/
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