pairwisePlot: Pairwise comparison plot

In elulu3/LymphoSeqTest: 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 or Bhattacharyya matrix can be found here: similarityMatrix and bhattacharyyaMatrix

Examples

file_path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq2")

stable <- readImmunoSeq(path = file_path)

atable <- productiveSeq(stable, aggregate = "junction_aa")

similarity_matrix <- scoringMatrix(productive_table = atable, mode="Similarity")

pairwisePlot(matrix = similarity_matrix)

bhattacharyya_matrix <- scoringMatrix(productive_table = atable, mode="Bhattacharyya")

pairwisePlot(matrix = bhattacharyya_matrix)

# Change plot color, title legend, and add title
pairwisePlot(matrix = similarity_matrix) + 
ggplot2::scale_fill_gradient(low = "#deebf7", high = "#3182bd") + 
ggplot2::labs(fill = "Similarity score") + 
ggplot2::ggtitle("Figure Title")

elulu3/LymphoSeqTest documentation built on Aug. 27, 2022, 5:47 a.m.