Af_compare_PLM: Function to compare the distributions of the Protein Language...

In AntibodyForests: Delineating Inter- And Intra-Antibody Repertoire Evolution

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.

Description

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.

Usage

Af_compare_PLM(PLM_dataframe, values, font.size, output.file)

Arguments

PLM_dataframe	Dataframe resulting from Af_PLM_dataframe(). This contains the Protein Language Model probabilities and ranks of the mutations along the edges of B cell lineage trees.
values	What values to compare "substitution_rank" will compare the rank of the mutation along the edge of the tree (Highest probability is rank 1). "substitution_probability" will copmare the probability of the mutation along the edge of the tree. "original_rank" will compare the rank of the original amino acid at the site of mutation along the edge of the tree (Highest probability is rank 1). "original_probability" will compare the probability of the original amino acid at the site of mutation along the edge of the tree. "unmutated_rank" will compare the rank of the unmutated amino acids along the edge of the tree (Highest probability is rank 1). "unmutated_probability" will compare the probabilities of the unmutated amino acids along the edge of the tree.
font.size	Font size for the plot. Default is 16.
output.file	string - specifies the path to the output file (PNG of PDF). Defaults to NULL.

Value

A pheatmap of the Jensen-Shannon distance between repertoires

Examples

Af_compare_PLM(PLM_dataframe = AntibodyForests::PLM_dataframe,
            values = "original_probability")

AntibodyForests documentation built on Aug. 8, 2025, 6:49 p.m.