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phyloseq

Article on Improved Microbiome Analysis

McMurdie and Holmes (2014) Waste Not, Want Not: Why Rarefying Microbiome Data is Statistically Inadmissible PLoS Computational Biology 10(4): e1003531

Presubmission versions ahead of acceptance (2013): PDF version 2, PDF version 1

Latest peer-reviewed article about phyloseq

phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data (2013) PLoS ONE 8(4):e61217

Interface with microbio.me/qiime

See the microbio_me_qiime tutorial for more details and examples downloading and importing into phyloseq/R directly from this public database.

Other resources

The phyloseq project also has a number of supporting online resources, most of which can by found at the phyloseq home page, or from the phyloseq stable release page on Bioconductor.

To post feature requests or ask for help, try the phyloseq Issue Tracker.

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Version

Version

1.12.2

License

AGPL-3

Maintainer

Paul J McMurdie

Last Published

February 15th, 2017

Functions in phyloseq (1.12.2)

Replace OTU identifier names

data-GlobalPatterns

(Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)

Method extensions to extraction operator for phyloseq objects.

(Data) Small example dataset from a human esophageal community (2004)

Returns the intersection of species and samples for the components of x

Filter taxa based on across-sample OTU abundance criteria

Import function to read the now legacy-format QIIME OTU table.

import_RDP_cluster

Import RDP cluster file and return otu_table (abundance table).

Calculate the Jensen-Shannon Divergence (distance)

Generates a function for labeling bootstrap values on a phylogenetic tree.

Function to avoid plotting node labels

Retrieve phylogenetic tree (phylo-class) from object.

An S4 placeholder of the main phylogenetic tree class from the ape package.

Somewhat flexible tree-import function

reconcile_categories

Cleans absent levels in sample_data/data.frame.

show_mothur_cutoffs

Show cutoff values available in a mothur file.

sample_variables

Get the sample variables present in sample_data

Build or access the taxonomyTable.

Access taxa_are_rows slot from otu_table objects.

Make filter fun. the most abundant k taxa

Make filter fun. that returns the top f fraction of taxa in a sample.

estimate_richness

Summarize alpha diversity

envHash2otu_table

Convert a sequence-sample hash (like ENV file) into an OTU table.

get_taxa_unique

Get a unique vector of the observed taxa at a particular taxonomic rank

Returns all abundance values for species i.

taxa_are_rows<-

Manually change taxa_are_rows through assignment.

import_mothur_constaxonomy

Import mothur constaxonomy file and return a taxonomyTable

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.

Universal import method (wrapper) for phyloseq-package

nodeplotdefault

Generates a default node-label function

Force index order of phyloseq objects

Get the number of samples.

parse_taxonomy_default

Parse elements of a taxonomy vector

S3 class for ape-calculated MDS results

Plot alpha diversity, flexibly with ggplot2

Generic plot defaults for phyloseq.

Replace OTU identifier names

Assign a (new) Taxonomy Table to x

General distance / dissimilarity index calculator

Calculate Double Principle Coordinate Analysis (DPCoA) using phylogenetic distance

Returns all abundance values of sample i.

Import new RDP OTU-table format

Get the values for a particular variable in sample_data

import_usearch_uc

Import usearch table format (.uc) to OTU table

S3 class placeholder definition (list) for metaMDS

Merge a subset of the species in x into one species/taxa/OTU.

Build or access the otu_table.

otu_table-class

The S4 class for storing taxa-abundance information.

Build phyloseq-class objects from their components.

phyloseq-package

Handling and analysis of high-throughput phylogenetic sequence data.

Create an ecologically-organized heatmap using ggplot2 graphics

Universal slot accessor function for phyloseq-class.

Assign a new OTU Table to x

data-enterotype

(Data) Enterotypes of the human gut microbiome (2011)

Constrained Correspondence Analysis and Redundancy Analysis.

Estimate the gap statistic on an ordination result

genefilter_sample

Filter OTUs with arbitrary function, sample-wise.

Microbiome Network Plot using ggplot2

Define a subset of samples to keep in a phyloseq object.

Prune unwanted OTUs / taxa from a phylogenetic object.

method extensions to show for phyloseq objects.

Agglomerate taxa of the same type.

Subset species by taxonomic expression

splat.phyloseq.objects

Convert phyloseq-class into a named list of its non-empty components.

get.component.classes

Show the component objects classes and slot names.

getslots.phyloseq

Return the non-empty slot names of a phyloseq object.

import_mothur_otulist

Import mothur list file and return as list object in R.

import_mothur_shared

Import mothur shared file and return an otu_table

Multiple testing of taxa abundance according to sample categories/classes

General ordination eigenvalue plotter using ggplot2.

microbio_me_qiime

Download and import directly from microbio.me/qiime

Plot a phylogenetic tree with optional annotations

Assign a (new) phylogenetic tree to x

Assign (new) sample_data to x

export_env_file

Export environment (ENV) file for UniFrac Server.

Get sample names.

read_tree_greengenes

Read GreenGenes tree released in annotated newick format

rarefy_even_depth

Resample an OTU table such that all samples have the same library size.

Returns the total number of individuals observed from each sample.

taxonomyTable-class

An S4 class that holds taxonomic classification data as a character matrix.

Thresholded rank transformation.

Make filter fun. that returns the most abundant p fraction of taxa

transform_sample_counts

Transform abundance data in an otu_table, sample-by-sample.

export_mothur_dist

Export a distance object as .names and .dist files for mothur

Import phyloseq data from biom-format file

import_env_file

Read a UniFrac-formatted ENV file.

import_qiime_otu_tax

Import now legacy-format QIIME OTU table as a list of two matrices.

import_qiime_sample_data

Import just sample_data file from QIIME pipeline.

Merge arguments into one phyloseq object.

Merge samples based on a sample variable or factor.

The main experiment-level class for phyloseq data

phyloseq-deprecated

Depcrecated functions in the phyloseq package.

Microbiome Network Plot using ggplot2

Retrieve reference sequences (XStringSet-class) from object.

plot_ordination

General ordination plotter based on ggplot2.

Set to FALSE any outlier species greater than f fractional abundance.

sample_data-class

The S4 for storing sample variables.

Build or access sample_data.

A closure version of the threshrank function.

Agglomerate closely-related taxa using single-linkage clustering.

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

build_tax_table

Build a tax_table from a named possibly-jagged list

capscale.phyloseq

Constrained Analysis of Principal Coordinates, capscale.

S3 class placeholder definition (list) for decorana

(Data) Reproducibility of soil microbiome data (2011)

filterfun_sample

A sample-wise filter function builder analogous to filterfun.

Method for fixing problems with phylo-class trees in phyloseq

Make microbiome network (igraph)

import_mothur_groups

Parse mothur group file into a simple hash table.

Get the number of taxa/species.

merge_phyloseq_pair

Merge pair of phyloseq component data objects of the same class.

import_mothur_otu_table

Import mothur list and group files and return an otu_table

Perform an ordination on phyloseq data

phyloseq_to_deseq2

Convert phyloseq data to DESeq2 dds object

S3 class placeholder definition (list) for phylogenetic trees.

A flexible, informative barplot phyloseq data

Create a ggplot summary of gap statistic results

Retrieve the names of the taxonomic ranks

Melt phyloseq data object into large data.frame

subset_ord_plot

Subset points from an ordination-derived ggplot

Subset samples by sample_data expression

Get species / taxa names.

Returns the total number of individuals observed from each species/taxa/OTU.

Transpose otu_table-class or phyloseq-class

Returns a data table defining the line segments of a phylogenetic tree.