adjust_span             Recursively adjust the LOESS span to ensure a
                        stable fit
apply_LOESS             Apply LOESS smoothing to barcode trajectories
calculateDiversity      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
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
