# pairwisePlot: Pairwise comparison plot In davidcoffey/LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

## Description

Creates a heat map from a similarity or Bhattacharyya matrix.

## Usage

 `1` ```pairwisePlot(matrix) ```

## Arguments

 `matrix` A similarity or Bhattacharyya matrix produced by the LymphoSeq functions similarityMatrix or bhattacharyyaMatrix.

## 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.

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`
 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18``` ```file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq") file.list <- readImmunoSeq(path = file.path) productive.aa <- productiveSeq(file.list = file.list, aggregate = "aminoAcid") similarity.matrix <- similarityMatrix(productive.seqs = productive.aa) pairwisePlot(matrix = similarity.matrix) bhattacharyya.matrix <- bhattacharyyaMatrix(productive.seqs = productive.aa) 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") ```