Handling and analysis of high-throughput microbiome census data

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Documentation for package ‘phyloseq’ version 1.50.0

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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.