Update the bugfixes branch

.gitignore

@@ -0,0 +1,15 @@
+CLAUDE.md
+
+# macOS resource forks and metadata
+.DS_Store
+._.DS_Store
+._*
+
+# vignette build artifacts (rendered HTMLs in vignettes/ dir)
+vignettes/*.html
+
+# Claude Code internal directory
+.claude/
+
+# scratch / legacy
+old/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: compact
 Title: compact
-Version: 0.0.3
+Version: 0.1.0
 Authors@R: c(
     person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7768-4856")),
@@ -28,6 +28,7 @@ Imports:
     xgboost (>= 1.7.11.1),
     SHAPforxgboost (>= 0.1.3),
     ggplot2,
+    ggrepel,
     data.table,
     ggrastr,
     pbapply,

NAMESPACE

@@ -16,11 +16,15 @@ export(FindShapKeyDriver)
 export(HeatmapDistance)
 export(LoadAlertSystem)
 export(LoadAlertSystemPathways)
+export(MacrostateTransitions)
 export(ModelZINB)
 export(ModulePerturbation)
 export(PerturbationLog2FC)
 export(PerturbationTransitions)
 export(PerturbationVectors)
+export(PlotMacrostateTransitions)
+export(PlotMarkovEmbedding)
+export(PlotMarkovScatter)
 export(PlotTransitionVectors)
 export(PredictAttractors)
 export(PredictCommitment)
@@ -52,13 +56,28 @@ importFrom(dplyr,rename)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,coord_fixed)
 importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_line)
+importFrom(ggplot2,element_rect)
 importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_hline)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_smooth)
+importFrom(ggplot2,geom_text)
 importFrom(ggplot2,geom_tile)
+importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_color_discrete)
+importFrom(ggplot2,scale_color_gradientn)
+importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_fill_gradientn)
+importFrom(ggplot2,scale_x_discrete)
+importFrom(ggplot2,scale_y_discrete)
 importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_minimal)
+importFrom(ggrepel,geom_label_repel)
 importFrom(igraph,components)
 importFrom(igraph,graph_from_adjacency_matrix)
 importFrom(methods,as)

NEWS.md

@@ -1,3 +1,14 @@
+# 0.1.0 (05-20-2026)
+## Added
+- `MacrostateTransitions` and `PlotMacrostateTransitions`: coarse-grain the cell-level transition probability matrix into a K × K group-level summary, with a stability index on the diagonal and a heatmap visualization.
+- `CombinePerturbAssays`: combine multiple perturbation assays by additive delta superposition into a single composite assay.
+- New vignette: **Basics — Simulated Branching Trajectory** (`simulation_tutorial`) covering the full `ModulePerturbation` workflow, graph connectivity checks, expression inspection, vector fields, macrostate transitions, and Markov chain analyses.
+- New vignette: **Advanced Use Cases — NSCLC CD8+ T Cells** (`advanced_NSCLC`) demonstrating step-by-step use of `ApplyPerturbation`, `ApplyPropagation`, and `PerturbationTransitions` with a custom gene set, a pseudobulk Pearson correlation network, `CustomPerturbation`, and `CombinePerturbAssays`.
+- pkgdown documentation site updated with both new vignettes.
+
+## Changes
+- None
+
 # 0.0.3 (02-20-2025)
 ## Added
 - New functions for cell fate analysis: `PredictPerturbationTime`, `PredictAttractors`, `PredictFates`, and `PredictCommitment`.