pairwisePlot: Pairwise comparison plot

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

Pairwise comparison plot

Description

Creates a heat map from a Bhattacharyya, Similarity, Sorensen, or PSI matrix.

Usage

pairwisePlot(matrix)

Arguments

matrix

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

Details

The plot is made using the package ggplot2 and can be reformatted using ggplot2 functions. See examples below.

Value

A pairwise comparison heat map.

See Also

An excellent resource for examples on how to reformat a ggplot can be found in the R Graphics Cookbook online (http://www.cookbook-r.com/Graphs/). The functions to create the similarity matrices can be found here: scoringMatrix()

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,
 aggregate = "junction_aa")
# Plot similarity using Similarity score
similarity_matrix <- LymphoSeq2::scoringMatrix(
  productive_table = amino_table,
  mode = "Similarity"
)
LymphoSeq2::pairwisePlot(matrix = similarity_matrix)
# Plot similarity using Bhattacharyya score
bhattacharyya_matrix <- LymphoSeq2::scoringMatrix(
  productive_table = amino_table,
  mode = "Bhattacharyya"
)
LymphoSeq2::pairwisePlot(matrix = bhattacharyya_matrix)
# Change plot color, title legend, and add title
LymphoSeq2::pairwisePlot(matrix = similarity_matrix) +
  ggplot2::scale_fill_gradient(low = "#deebf7", high = "#3182bd") +
  ggplot2::labs(fill = "Similarity score") +
  ggplot2::ggtitle("Pairwise similarity score")

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