parsePhyloseq: parsePhyloseq

In lch14forever/microbiomeViz:

Description

This function takes a phyloseq-class and parse it to a treedata object, that can be further visualized by the tree.backbone function. The tax_table slot must not be empty in the phyloseq object.

Usage

parsePhyloseq(
  physeq,
  use_abundance = TRUE,
  node.size.scale = 1,
  node.size.offset = 1
)

Arguments

physeq	A phyloseq object. The tax_table slot must not be empty.
use_abundance	Boolean variable whether to set node sizes according to abundance. If FALSE, all nodes will have the same size.
node.size.scale	the parameter 'a' controlling node size: nodeSize=a*log(relative_abundance)+b
node.size.offset	the parameter 'b' controlling node size: nodeSize=a*log(relative_abundance)+b

Value

a treeio::treedata object

Author(s)

Chenghao Zhu, Chenhao Li, Guangchuang Yu

See Also

tree.backbone, parseMetaphlanTSV, phyloseq-class

Examples

data("GlobalPatterns")
GP = GlobalPatterns
otu_table = otu_table(GP)
tax_table = tax_table(GP)

# Use the OTUs that make up 99% of the total
lib_size = colSums(otu_table)
mat = sapply(1:ncol(otu_table), function(i)
    otu_table[,i]/lib_size[i] >= 0.01)
ind = rowSums(mat)>=1

otu_table = otu_table[ind,]
tax_table = tax_table[ind,]

physeq = phyloseq(otu_table, tax_table) %>%
    fix_duplicate_tax()

tr = parsePhyloseq(physeq, use_abundance = F)
p = tree.backbone(tr, size=1)

lch14forever/microbiomeViz documentation built on Sept. 7, 2020, 4:34 p.m.