LymphoSeq (version 1.0.2)

pairwisePlot: 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.

Value

A pairwise comparison heat map.

Details

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

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")