plotHummanMetadata: plotHummanMetadata

Description Usage Arguments

View source: R/humann2_utils.R

Description

outputs order of samples by bray curtis

Usage

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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.