# Handling and analysis of high-throughput microbiome census data

## Documentation for package ‘phyloseq’ version 1.55.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B D E F G I M N O P R S T U misc

phyloseq-deprecated-package | Depcrecated functions in the phyloseq package.
phyloseq-package | Handling and analysis of high-throughput phylogenetic sequence data.

## -- A --

access | Universal slot accessor function for phyloseq-class.
assign-otu_table | Assign a new OTU Table to 'x'
assign-phy_tree | Assign a (new) phylogenetic tree to 'x'
assign-sample_data | Assign (new) sample_data to 'x'
assign-sample_names | Replace OTU identifier names
assign-taxa_are_rows | Manually change taxa_are_rows through assignment.
assign-taxa_names | Replace OTU identifier names
assign-tax_table | Assign a (new) Taxonomy Table to 'x'

## -- B --

build_tax_table | Build a 'tax_table' from a named possibly-jagged list

## -- D --

data-enterotype | (Data) Enterotypes of the human gut microbiome (2011)
data-esophagus | (Data) Small example dataset from a human esophageal community (2004)
data-GlobalPatterns | (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)
data-soilrep | (Data) Reproducibility of soil microbiome data (2011)
deprecated_phyloseq_function | Depcrecated functions in the phyloseq package.
dist-class | An S4 placeholder for the 'dist' class.
distance | Calculate distance, dissimilarity
distance-method | Calculate distance, dissimilarity
distanceMethodList | List of distance method keys supported in 'distance'
DPCoA | Calculate Double Principle Coordinate Analysis (DPCoA) using phylogenetic distance

## -- E --

enterotype | (Data) Enterotypes of the human gut microbiome (2011)
esophagus | (Data) Small example dataset from a human esophageal community (2004)
estimate_richness | Summarize alpha diversity
export_env_file | Export environment (ENV) file for UniFrac Server.
export_mothur_dist | Export a distance object as '.names' and '.dist' files for mothur

## -- F --

filterfunSample | Depcrecated functions in the phyloseq package.
filterfun_sample | A sample-wise filter function builder analogous to 'filterfun'.
filter_taxa | Filter taxa based on across-sample OTU abundance criteria

## -- G --

gapstat_ord | Estimate the gap statistic on an ordination result
genefilterSample | Depcrecated functions in the phyloseq package.
genefilter_sample | Filter OTUs with arbitrary function, sample-wise.
genefilter_sample-method | Filter OTUs with arbitrary function, sample-wise.
getSamples | Depcrecated functions in the phyloseq package.
getslots.phyloseq | Return the non-empty slot names of a phyloseq object.
getSpecies | Depcrecated functions in the phyloseq package.
getTaxa | Depcrecated functions in the phyloseq package.
getVariable | Depcrecated functions in the phyloseq package.
get_sample | Returns all abundance values for species 'i'.
get_sample-method | Returns all abundance values for species 'i'.
get_taxa | Returns all abundance values of sample 'i'.
get_taxa-method | Returns all abundance values of sample 'i'.
get_taxa_unique | Get a unique vector of the observed taxa at a particular taxonomic rank
get_variable | Get the values for a particular variable in sample_data
GlobalPatterns | (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)

## -- I --

import | Universal import method (wrapper) for phyloseq-package
import_biom | Import phyloseq data from biom-format file
import_env_file | Read a UniFrac-formatted ENV file.
import_mothur | General function for importing mothur data files into phyloseq.
import_mothur_dist | Import mothur-formatted distance file
import_pyrotagger_tab | Imports a tab-delimited version of the pyrotagger output file.
import_qiime | Import function to read the now legacy-format QIIME OTU table.
import_qiime_otu_tax | Import now legacy-format QIIME OTU table as a list of two matrices.
import_qiime_sampleData | Depcrecated functions in the phyloseq package.
import_qiime_sample_data | Import just 'sample_data' file from QIIME pipeline.
import_RDP_cluster | Import RDP cluster file and return otu_table (abundance table).
import_RDP_otu | Import new RDP OTU-table format
import_uparse | Import UPARSE file format
import_usearch_uc | Import usearch table format ('.uc') to OTU table

## -- M --

make_network | Make microbiome network (igraph)
merge_phyloseq | Merge arguments into one phyloseq object.
merge_phyloseq_pair | Merge pair of phyloseq component data objects of the same class.
merge_phyloseq_pair-method | Merge pair of phyloseq component data objects of the same class.
merge_samples | Merge samples based on a sample variable or factor.
merge_samples-method | Merge samples based on a sample variable or factor.
merge_species | Depcrecated functions in the phyloseq package.
merge_taxa | Merge a subset of the species in 'x' into one species/taxa/OTU.
merge_taxa-method | Merge a subset of the species in 'x' into one species/taxa/OTU.
microbio_me_qiime | Import microbio.me/qiime (QIIME-DB) data package
mt | Multiple testing of taxa abundance according to sample categories/classes
mt-method | Multiple testing of taxa abundance according to sample categories/classes

## -- N --

nodeplotblank | Function to avoid plotting node labels
nodeplotboot | Generates a function for labeling bootstrap values on a phylogenetic tree.
nodeplotdefault | Generates a default node-label function
nsamples | Get the number of samples.
nsamples-method | Get the number of samples.
nspecies | Depcrecated functions in the phyloseq package.
ntaxa | Get the number of taxa/species.
ntaxa-method | Get the number of taxa/species.

## -- O --

ordinate | Perform an ordination on phyloseq data
otuTable | Depcrecated functions in the phyloseq package.
otuTable<- | Depcrecated functions in the phyloseq package.
otu_table | Build or access the otu_table.
otu_table-class | The S4 class for storing taxa-abundance information.
otu_table-method | Build or access the otu_table.
otu_table<- | Assign a new OTU Table to 'x'
otu_table<--method | Assign a new OTU Table to 'x'

## -- P --

parse_taxonomy_default | Parse elements of a taxonomy vector
parse_taxonomy_greengenes | Parse elements of a taxonomy vector
parse_taxonomy_qiime | Parse elements of a taxonomy vector
phylo-class | An S4 placeholder of the main phylogenetic tree class from the ape package.
phyloseq | Build phyloseq-class objects from their components.
phyloseq-class | The main experiment-level class for phyloseq data
phyloseq-deprecated | Depcrecated functions in the phyloseq package.
phyloseq_to_deseq2 | Convert phyloseq data to DESeq2 dds object
phyloseq_to_metagenomeSeq | Convert phyloseq data to MetagenomeSeq MRexperiment object
phy_tree | Retrieve phylogenetic tree ('phylo'-class) from object.
phy_tree-method | Retrieve phylogenetic tree ('phylo'-class) from object.
phy_tree<- | Assign a (new) phylogenetic tree to 'x'
phy_tree<--method | Assign a (new) phylogenetic tree to 'x'
plot_bar | A flexible, informative barplot phyloseq data
plot_clusgap | Create a ggplot summary of gap statistic results
plot_heatmap | Create an ecologically-organized heatmap using ggplot2 graphics
plot_net | Microbiome Network Plot using ggplot2
plot_network | Microbiome Network Plot using ggplot2
plot_ordination | General ordination plotter based on ggplot2.
plot_phyloseq | Generic plot defaults for phyloseq.
plot_phyloseq-method | Generic plot defaults for phyloseq.
plot_richness | Plot alpha diversity, flexibly with ggplot2
plot_richness_estimates | Depcrecated functions in the phyloseq package.
plot_scree | General ordination eigenvalue plotter using ggplot2.
plot_taxa_bar | Depcrecated functions in the phyloseq package.
plot_tree | Plot a phylogenetic tree with optional annotations
prune_samples | Define a subset of samples to keep in a phyloseq object.
prune_samples-method | Define a subset of samples to keep in a phyloseq object.
prune_species | Depcrecated functions in the phyloseq package.
prune_taxa | Prune unwanted OTUs / taxa from a phylogenetic object.
prune_taxa-method | Prune unwanted OTUs / taxa from a phylogenetic object.
psmelt | Melt phyloseq data object into large data.frame

## -- R --

rank.names | Depcrecated functions in the phyloseq package.
rank_names | Retrieve the names of the taxonomic ranks
rarefy_even_depth | Resample an OTU table such that all samples have the same library size.
read_tree | Somewhat flexible tree-import function
read_tree_greengenes | Read GreenGenes tree released in annotated newick format
refseq | Retrieve reference sequences ('XStringSet'-class) from object.
refseq-method | Retrieve reference sequences ('XStringSet'-class) from object.
rm_outlierf | Set to FALSE any outlier species greater than f fractional abundance.

## -- S --

samData | Depcrecated functions in the phyloseq package.
sample.names | Depcrecated functions in the phyloseq package.
sample.variables | Depcrecated functions in the phyloseq package.
sampleData | Depcrecated functions in the phyloseq package.
sampleData<- | Depcrecated functions in the phyloseq package.
sampleNames | Depcrecated functions in the phyloseq package.
sampleSums | Depcrecated functions in the phyloseq package.
sample_data | Build or access sample_data.
sample_data-class | The S4 for storing sample variables.
sample_data-method | Build or access sample_data.
sample_data<- | Assign (new) sample_data to 'x'
sample_names | Get sample names.
sample_names-method | Get sample names.
sample_names<- | Replace OTU identifier names
sample_names<--method | Replace OTU identifier names
sample_sums | Returns the total number of individuals observed from each sample.
sample_variables | Get the sample variables present in sample_data
sam_data | Depcrecated functions in the phyloseq package.
sam_data<- | Depcrecated functions in the phyloseq package.
show-method | method extensions to show for phyloseq objects.
show_mothur_cutoffs | Show cutoff values available in a mothur file.
show_mothur_list_cutoffs | Depcrecated functions in the phyloseq package.
soilrep | (Data) Reproducibility of soil microbiome data (2011)
species.names | Depcrecated functions in the phyloseq package.
speciesAreRows | Depcrecated functions in the phyloseq package.
speciesarerows | Depcrecated functions in the phyloseq package.
speciesAreRows<- | Depcrecated functions in the phyloseq package.
speciesSums | Depcrecated functions in the phyloseq package.
subset_ord_plot | Subset points from an ordination-derived ggplot
subset_samples | Subset samples by sample_data expression
subset_species | Depcrecated functions in the phyloseq package.
subset_taxa | Subset species by taxonomic expression

## -- T --

t | Transpose 'otu_table-class' or 'phyloseq-class'
t-method | Transpose 'otu_table-class' or 'phyloseq-class'
taxaplot | Depcrecated functions in the phyloseq package.
taxa_are_rows | Access taxa_are_rows slot from otu_table objects.
taxa_are_rows-method | Access taxa_are_rows slot from otu_table objects.
taxa_are_rows<- | Manually change taxa_are_rows through assignment.
taxa_are_rows<--method | Manually change taxa_are_rows through assignment.
taxa_names | Get species / taxa names.
taxa_names-method | Get species / taxa names.
taxa_names<- | Replace OTU identifier names
taxa_names<--method | Replace OTU identifier names
taxa_sums | Returns the total number of individuals observed from each species/taxa/OTU.
taxglom | Depcrecated functions in the phyloseq package.
taxonomyTable-class | An S4 class that holds taxonomic classification data as a character matrix.
taxTab | Depcrecated functions in the phyloseq package.
taxtab | Depcrecated functions in the phyloseq package.
taxTab<- | Depcrecated functions in the phyloseq package.
tax_glom | Agglomerate taxa of the same type.
tax_table | Build or access the taxonomyTable.
tax_table-method | Build or access the taxonomyTable.
tax_table<- | Assign a (new) Taxonomy Table to 'x'
tax_table<--method | Assign a (new) Taxonomy Table to 'x'
threshrank | Thresholded rank transformation.
threshrankfun | A closure version of the 'threshrank' function.
tipglom | Depcrecated functions in the phyloseq package.
tip_glom | Agglomerate closely-related taxa using single-linkage clustering.
topf | Make filter fun. that returns the top f fraction of taxa in a sample.
topk | Make filter fun. the most abundant 'k' taxa
topp | Make filter fun. that returns the most abundant 'p' fraction of taxa
transformSampleCounts | Transform abundance data in an 'otu_table', sample-by-sample.
transform_sample_counts | Transform abundance data in an 'otu_table', sample-by-sample.
tre | Depcrecated functions in the phyloseq package.
tre<- | Depcrecated functions in the phyloseq package.
tree_layout | Returns a data table defining the line segments of a phylogenetic tree.

## -- U --

UniFrac | Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs.
UniFrac-method | Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs.

## -- misc --

[-method | Method extensions to extraction operator for phyloseq objects.