pairwiseNetwork: Pairwise comparison network graph

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

Pairwise comparison network graph

Description

Creates a network graph from a Bhattacharyya, Similarity, Sorensen, or PSI matrix.

Usage

pairwiseNetwork(matrix)

Arguments

matrix

A Bhattacharyya, Similarity, Sorensen, or PSI matrix produced by the LymphoSeq2 scoringMatrix() function.

Value

A network graph visualizing pairwise comparisons. The thicker the line connecting two nodes, the greater the similarity.

Examples

file_path <- system.file("extdata", "TCRB_sequencing",
  package = "LymphoSeq2"
)
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1)
study_table <- LymphoSeq2::topSeqs(study_table, top = 100)
amino_table <- LymphoSeq2::productiveSeq(
  study_table = study_table,
  aggregate = "junction_aa"
)
matrix <- LymphoSeq2::scoringMatrix(amino_table, mode = "Similarity")
network_graph <- LymphoSeq2::pairwiseNetwork(matrix)

shashidhar22/LymphoSeq2 documentation built on Jan. 16, 2024, 4:29 a.m.