| adjust_span | Recursively adjust the LOESS span to ensure a stable fit |
| applyLOESS | Quantify and Visualize Hierarchical Clustering Results |
| apply_LOESS | Apply LOESS smoothing to barcode trajectories |
| calculateDiversity | Calculate diversity indices for a sample |
| calculate_diversity | Calculate diversity indices for a sample |
| calculate_q_0 | Calculate diversity indices for a sample |
| calculate_q_1 | Calculate diversity indices for a sample |
| calculate_q_inf | Calculate diversity indices for a sample |
| fetchTop | Fetch Top Barcodes by Maximum Frequency |
| filterData | Filter Lineage Data for Clustering |
| filterHC | Filter Hierarchical Clusters Based on Size and Dominance |
| format_sample | Calculate diversity indices for a sample |
| melt_dist | Quantify and Visualize Hierarchical Clustering Results |
| performHClustering | Perform Hierarchical Clustering on Barcoded Lineages |
| plotClusterLog10 | Plot individual barcode frequencies (log10) for a single cluster |
| plotClustersAndLoess | Plot the log10-transformed barcode frequencies and the moving averages (LOESS) |
| plotDiversity | Plot diversity dynamics over time |
| plotDynamics | Plot barcode dynamics |
| plotHCQuantification | Quantify and Visualize Hierarchical Clustering Results |
| reshapeData | Reshape Barcode Abundance Data to Frequency Format |
| theme_Matrix | Theme for matrix-style plots (e.g. heatmaps or abundance matrices) |
| theme_Publication | Custom ggplot2 theme for publication-style figures |
| theme_Publication_noYaxis | Custom ggplot2 theme with no y-axis title |