pairwisePlot {LymphoSeq} | R Documentation

## Pairwise comparison plot

### Description

Creates a heat map from a similarity or Bhattacharyya matrix.

### Usage

    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.

### 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 = "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")

[Package LymphoSeq version 1.12.0 Index]