plotHummanMetadata: plotHummanMetadata

In philippmuench/PMtools: Miscellaneous helper functions

Description

outputs order of samples by bray curtis

Usage

plotHummanMetadata(
  metaphlan,
  distance.method = "bray",
  cluster.method = "single",
  metadata = hmp1_2_metadata
)

Arguments

metaphlan	MetaPhlAn2 table
distance.method	Dissimilarity index, partial match to "manhattan", "euclidean", "canberra", "clark", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial", "chao", "cao" or "mahalanobis".
cluster.method	The agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).

philippmuench/PMtools documentation built on Dec. 27, 2019, 8:08 a.m.