# Delineating Inter- And Intra-Antibody Repertoire Evolution

## Documentation for package ‘AntibodyForests’ version 1.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

Af_add_node_feature | Function to add node features to an AntibodyForests-object
Af_build | Function to infer B cell evolutionary networks for all clonotypes in VDJ dataframe as obtained from the 'VDJ_build()' function.
Af_cluster_metrics | Function to make a grouped boxplot of metrics from clusters of clonotypes
Af_cluster_node_features | Function to create a barplot of the cluster composition of selected features from each tree in an AntibodyForests-object
Af_compare_across_repertoires | A function to compare dynamics of B cell evolution across different repertoires.
Af_compare_methods | Function to compare trees created with different algorithms from the same clonotype.
Af_compare_PLM | Function to compare the distributions of the Protein Language Model probabilities or ranks of the mutations along the edges of B cell lineage trees across repertoires using the Jensen-Shannon divergence.
Af_compare_within_repertoires | Function to compare tree topology of B cell lineages
af_default | Small AntibodyForests object with default algorithm for function testing purposes
Af_distance_boxplot | Function to make a grouped boxplot of distance between nodes from specific groups and the germline of lineage trees constructed with AntibodyForests.
Af_distance_scatterplot | Function to scatterplot the distance to the germline to a numerical node feature of the AntibodyForests-object
Af_edge_RMSD | Function to calculate the RMSD between sequences over each edge in the AntibodyForest object
Af_get_sequences | Function to get the sequences from the nodes in an AntibodyForest object
Af_metrics | Function to calculate metrics for each tree in an AntibodyForests-object
af_mst | Small AntibodyForests object with MST algorithm for function testing purposes
af_nj | Small AntibodyForests object with NJ algorithm for function testing purposes
Af_node_size_boxplot | Function to make a grouped boxplot of the normalized average node sizes (number of cells with the exact same sequence) from specific groups of lineage trees constructed with AntibodyForests.
Af_PLM_dataframe | Function to create a dataframe of the Protein Language Model probabilities and ranks of the mutations along the edges of B cell lineage trees.
Af_plot_PLM | Function to create a distribution plot of the Protein Language Model probabilities and ranks of the mutations along the edges of B cell lineage trees.
Af_plot_PLM_mut_vs_cons | Function to create a boxplot of the Protein Language Model probabilities
Af_plot_tree | Plots lineage tree of clonotype from AntibodyForests object
Af_sync_nodes | Function to synchronize the node labels/names of all clonotypes within all samples of two AntibodyForests objects.
Af_to_newick | Saves an AntibodyForests-object into a newick file
calculate_GBLD | Calculate the GBLD distance between trees in an AntibodyForests object. Code is derived from https://github.com/tahiri-lab/ClonalTreeClustering/blob/main/src/Python/GBLD_Metric_Final.ipynb Farnia, M., Tahiri, N. New generalized metric based on branch length distance to compare B cell lineage trees. Algorithms Mol Biol 19, 22 (2024). https://doi.org/10.1186/s13015-024-00267-1
compare_repertoire | Example output from Af_compare_within_repertoires() for function testing purposes
igraph_to_phylo | Converts an igraph network into a phylogenetic tree as a phylo object.
newick_to_Af | Converts files with phylogenetic trees in newick format into an AntibodyForests object.
PLM_dataframe | Small PLM dataframe for function testing purposes
small_af | Small AntibodyForests object for function testing purposes
small_vdj | Small VDJ dataframe for function testing purposes
VDJ_3d_properties | Function to calculate 3D-structure propoperties such as the average charge and hydrophobicity, pKa shift, free energy, RMSD of PDB files and add them to an AntibodyForests-object
VDJ_import_IgBLAST_annotations | Function to import the annotations and alignments from IgBLAST output into the VDJ dataframe.
VDJ_integrate_bulk | A function to integrate bulk and single cell data
VDJ_to_AIRR | Function to convert VDJ dataframe into an AIRR-formatted TSV file.