pairwisePlot: Pairwise comparison plot

Description Usage Arguments Details Value See Also Examples

View source: R/pairwisePlot.R

Description

Creates a heat map from a similarity or Bhattacharyya matrix.

Usage

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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

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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")

davidcoffey/LymphoSeq documentation built on Dec. 31, 2019, 9:52 p.m.