hierarchy-tree: Calculate hierarchy tree

In microbiome/mia: Microbiome analysis

Calculate hierarchy tree

Description

These functions generate a hierarchy tree using taxonomic information from a SummarizedExperiment object and add this hierarchy tree into the rowTree.

Usage

getHierarchyTree(x, ...)

## S4 method for signature 'SummarizedExperiment'
getHierarchyTree(x, ...)

addHierarchyTree(x, ...)

## S4 method for signature 'SummarizedExperiment'
addHierarchyTree(x, ...)

Arguments

x	TreeSummarizedExperiment.
...	optional arguments not used currently.

Details

addHierarchyTree calculates a hierarchy tree from the available taxonomic information and add it to rowTree.

getHierarchyTree generates a hierarchy tree from the available taxonomic information. Internally it uses toTree and resolveLoop to sanitize data if needed.

Please note that a hierarchy tree is not an actual phylogenetic tree. A phylogenetic tree represents evolutionary relationships among features. On the other hand, a hierarchy tree organizes species into a hierarchical structure based on their taxonomic ranks.

Value

• addHierarchyTree: a TreeSummarizedExperiment whose phylo tree represents the hierarchy among available taxonomy information.

• getHierarchyTree: a phylo tree representing the hierarchy among available taxonomy information.

Examples

# Generate a tree based on taxonomic rank hierarchy (a hierarchy tree).
data(GlobalPatterns)
tse <- GlobalPatterns
getHierarchyTree(tse)

# Add a hierarchy tree to a TreeSummarizedExperiment.
# Please note that any tree already stored in rowTree() will be overwritten.
tse <- addHierarchyTree(tse)
tse

microbiome/mia documentation built on Nov. 20, 2024, 1:12 a.m.