'doblin': Inferring Dominant Clonal Lineages from DNA Barcoding Time-Series

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Documentation for package ‘doblin’ version 0.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Code demos. Use demo() to run them.

Help Pages

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