pairwisePlot: Pairwise comparison plot

In LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

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")

Example output

Loading required package: LymphoSeqDB
sh: 1: cannot create /dev/null: Permission denied
sh: 1: wc: Permission denied
Could not detect number of cores, defaulting to 1.

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Scale for 'fill' is already present. Adding another scale for 'fill', which
will replace the existing scale.
Warning message:
system call failed: Cannot allocate memory 

LymphoSeq documentation built on Nov. 8, 2020, 8:09 p.m.