plotSimilarity: Plot similarity matrix between samples

In microresearcher/MicroVis: Microbiome Analysis and Visualization

Plot similarity matrix between samples

Description

Plot similarity matrix between samples

Usage

plotSimilarity(
  dataset = NULL,
  rank = NULL,
  dist_method = "bray",
  weighted = F,
  clust_method = "ward.D2",
  clust_num = 2,
  r_cutoff = 0
)

Arguments

dataset	MicroVis dataset. Defaults to the active dataset
rank	Rank of features to use for similarity calculation
dist_method	Dissimilarity calculation method. One of either "pearson", "spearman", bray", "euclidean", "jaccard", "unifrac", "manhattan", "canberra", "clark", "kulczynski", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial", "chao", "cao", "mahalanobis", "chisq" or "chord". Defaults to "bray"
weighted	If performing unifract distance, whether to use weighted or unweighted unifrac. Defults to FALSE (unweighted)
clust_method	Clustering method. One of either "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). Defaults to "ward.D2"
clust_num	Number of clusters to try to make
r_cutoff	R-values with absolute value below this cutoff will be shaded white. Defaults to 0

Value

Similarity matrix heatmap

microresearcher/MicroVis documentation built on Feb. 8, 2024, 10:59 a.m.