phyloseq_otu_occurrence: Estimate species occurrence (within groups of samples)

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Estimate species occurrence (within groups of samples)

Description

Estimate species occurrence (within groups of samples)

Usage

phyloseq_otu_occurrence(
  physeq,
  variable = NULL,
  taxa_frequency = "percentage",
  drop_zeroes = FALSE,
  justdf = FALSE,
  long = FALSE
)

Arguments

physeq	A phyloseq-class object
variable	Character string defining a variable name of the sample groups (this variable should be present in sample_data) or NULL (no sample groups)
taxa_frequency	Logical; if TRUE (default), relative frequency of species occurence within a sample group will be returned; if FALSE, number of samples within each sample group will be returned for each taxa
drop_zeroes	Logical; if TRUE, taxa with total zero abundance will be removed
justdf	Logical; if TRUE, return only a data frame with taxa occurrences; if FALSE (default), modified phyloseq object will be returned
long	Logical; if TRUE, data frame with taxa occurrences will be returned in long format (with a single column defining the sample group); if FALSE (default), species occurrences will be returned in a wide format (sample groups as columns)

Value

A phyloseq-class object (if justdf = FALSE) or a data frame (justdf = TRUE).

Examples

# Load data
data("GlobalPatterns")

## Return phyloseq-object with sample groups instead of samples
# With absolute counts (e.g., number of samples with the species)
gpa <- phyloseq_otu_occurrence(GlobalPatterns, variable = "SampleType", taxa_frequency = F)
gpa
head( otu_table(gpa) )

# With relative frequency of species occurence within a sample group
gpr <- phyloseq_otu_occurrence(GlobalPatterns, variable = "SampleType", taxa_frequency = T)
gpr
head( otu_table(gpr) )


## Return just a data frame with taxa occurrences
# In wide format (sample groups as columns)
gpw <- phyloseq_otu_occurrence(GlobalPatterns, variable = "SampleType", taxa_frequency = T, drop_zeroes = F, justdf = T, long = F)
head(gpw)

# In long format (with a single column with sample type)
gpl <- phyloseq_otu_occurrence(GlobalPatterns, variable = "SampleType", taxa_frequency = T, drop_zeroes = F, justdf = T, long = T)
head(gpl)

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.