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 |