R/plotPairwiseNetwork.R

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

#' Pairwise comparison network graph
#'
#' Creates a network graph from a Bhattacharyya, Similarity, Sorensen, or
#' PSI matrix.
# ;
#' @param matrix A Bhattacharyya, Similarity, Sorensen, or PSI matrix produced
#' by the LymphoSeq2 [scoringMatrix()] function.
#' @return 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)
#' @export
pairwiseNetwork <- function(matrix) {
  g <- igraph::graph_from_adjacency_matrix(matrix,
    mode = "undirected",
    weighted = TRUE, diag = FALSE
  )

  plot(g,
    layout = igraph::layout.circle,
    edge.width = igraph::E(g)$weight * 5,
    vertex.size = 10,
    vertex.label.cex = 1,
    vertex.label.dist = 2
  )
}