plotDissimilarityMatrix: create heatmap of pairwise distance matrix between samples

In ph-pham/RepSeq: Analysis of High-throughput sequencing repertoire data (RepSeqTools)

Description

function plot a heatmap of a squared distance matrix computed between samples

Usage

plotDissimilarityMatrix(
  x,
  level = c("VpJ", "V", "J", "VJ", "CDR3aa"),
  method = c("manhattan", "euclidean", "canberra", "clark", "bray", "kulczynski",
    "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial",
    "chao", "cao", "mahalanobis"),
  binary = FALSE
)

Arguments

x	an object of class RepSeqExperiment
level	a string of characters indicating the level at which performed all calculations.
method	distance computation method. Choose one among manhattan, euclidean, canberra, clark, bray, kulczynski, jaccard, gower, altGower, morisita, horn, mountford, raup, binomial, chao, cao, mahalanobis.
binary	if TRUE data will be transformed into present/absent data.

Value

a heatmap

Examples

## Not run: 
# The package RepSeqData contains example datasets 
library(RepSeqData)
# plot heatmap of dissimilarity matrix.
plotDissimilarityMatrix(x = RepSeqData, level = "V", method = "euclidean")

## End(Not run)

ph-pham/RepSeq documentation built on Dec. 22, 2021, 7:47 a.m.