pairwisePlot {LymphoSeq} | R Documentation |
Creates a heat map from a similarity or Bhattacharyya matrix.
pairwisePlot(matrix)
matrix |
A similarity or Bhattacharyya matrix produced by the LymphoSeq functions similarityMatrix or bhattacharyyaMatrix. |
The plot is made using the package ggplot2 and can be reformatted using ggplot2 functions. See examples below.
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
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")