phyloseq: Handling and analysis of high-throughput microbiome census data

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

AuthorPaul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain
Date of publicationNone
MaintainerPaul J. McMurdie <joey711@gmail.com>
LicenseAGPL-3
Version1.19.1
http://dx.plos.org/10.1371/journal.pone.0061217

View on Bioconductor

Man pages

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'

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

capscale-phyloseq-methods: Constrained Analysis of Principal Coordinates, 'capscale'.

cca-rda-phyloseq-methods: Constrained Correspondence Analysis and Redundancy Analysis.

chunkReOrder: Chunk re-order a vector so that specified newstart is first.

data-enterotype: (Data) Enterotypes of the human gut microbiome (2011)

data-esophagus: (Data) Small example dataset from a human esophageal...

data-GlobalPatterns: (Data) Global patterns of 16S rRNA diversity at a depth of...

data-soilrep: (Data) Reproducibility of soil microbiome data (2011)

decorana: S3 class placeholder definition (list) for decorana

distance: Calculate distance, dissimilarity

distanceMethodList: List of distance method keys supported in 'distance'

dist-class: An S4 placeholder for the 'dist' class.

DPCoA: Calculate Double Principle Coordinate Analysis (DPCoA) using...

envHash2otu_table: Convert a sequence-sample hash (like ENV file) into an OTU...

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...

extract-methods: Method extensions to extraction operator for phyloseq...

filterfun_sample: A sample-wise filter function builder analogous to...

filter_taxa: Filter taxa based on across-sample OTU abundance criteria

fix_phylo: Method for fixing problems with phylo-class trees in phyloseq

gapstat_ord: Estimate the gap statistic on an ordination result

genefilter_sample-methods: Filter OTUs with arbitrary function, sample-wise.

get.component.classes: Show the component objects classes and slot names.

get_sample-methods: Returns all abundance values for species 'i'.

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

get_taxa-methods: Returns all abundance values of sample 'i'.

get_taxa_unique: Get a unique vector of the observed taxa at a particular...

get_variable: Get the values for a particular variable in sample_data

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...

import_mothur_constaxonomy: Import mothur constaxonomy file and return a taxonomyTable

import_mothur_dist: Import mothur-formatted distance file

import_mothur_groups: Parse mothur group file into a simple hash table.

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

import_mothur_otu_table: Import mothur list and group files and return an otu_table

import_mothur_shared: Import mothur shared file and return an otu_table

import_pyrotagger_tab: Imports a tab-delimited version of the pyrotagger output...

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

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

import_qiime_sample_data: Import just 'sample_data' file from QIIME pipeline.

import_RDP_cluster: Import RDP cluster file and return otu_table (abundance...

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

index_reorder: Force index order of phyloseq objects

intersect_taxa: Returns the intersection of species and samples for the...

JSD: Calculate the Jensen-Shannon Divergence (distance)

make_network: Make microbiome network (igraph)

merge_phyloseq: Merge arguments into one phyloseq object.

merge_phyloseq_pair-methods: Merge pair of phyloseq component data objects of the same...

merge_samples-methods: Merge samples based on a sample variable or factor.

merge_taxa-methods: Merge a subset of the species in 'x' into one...

metaMDS: S3 class placeholder definition (list) for metaMDS

microbio_me_qiime: Import microbio.me/qiime (QIIME-DB) data package

mt-methods: Multiple testing of taxa abundance according to sample...

nodeplotblank: Function to avoid plotting node labels

nodeplotboot: Generates a function for labeling bootstrap values on a...

nodeplotdefault: Generates a default node-label function

nsamples-methods: Get the number of samples.

ntaxa-methods: Get the number of taxa/species.

ordinate: Perform an ordination on phyloseq data

otu_table-class: The S4 class for storing taxa-abundance information.

otu_table-methods: Build or access the otu_table.

parseTaxonomy-functions: Parse elements of a taxonomy vector

pcoa: S3 class for ape-calculated MDS results

phylo: S3 class placeholder definition (list) for phylogenetic...

phylo-class: An S4 placeholder of the main phylogenetic tree class from...

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-package: Handling and analysis of high-throughput phylogenetic...

phyloseq_to_deseq2: Convert phyloseq data to DESeq2 dds object

phyloseq_to_metagenomeSeq: Convert phyloseq data to MetagenomeSeq MRexperiment object

phy_tree-methods: Retrieve phylogenetic tree ('phylo'-class) from object.

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...

plot_net: Microbiome Network Plot using ggplot2

plot_network: Microbiome Network Plot using ggplot2

plot_ordination: General ordination plotter based on ggplot2.

plot_phyloseq-methods: Generic plot defaults for phyloseq.

plot_richness: Plot alpha diversity, flexibly with ggplot2

plot_scree: General ordination eigenvalue plotter using ggplot2.

plot_tree: Plot a phylogenetic tree with optional annotations

prune_samples-methods: Define a subset of samples to keep in a phyloseq object.

prune_taxa-methods: Prune unwanted OTUs / taxa from a phylogenetic object.

psmelt: Melt phyloseq data object into large data.frame

rank_names: Retrieve the names of the taxonomic ranks

rarefy_even_depth: Resample an OTU table such that all samples have the same...

read_tree: Somewhat flexible tree-import function

read_tree_greengenes: Read GreenGenes tree released in annotated newick format

reconcile_categories: Cleans absent levels in sample_data/data.frame.

refseq-methods: Retrieve reference sequences ('XStringSet'-class) from...

rm_outlierf: Set to FALSE any outlier species greater than f fractional...

sample_data-class: The S4 for storing sample variables.

sample_data-methods: Build or access sample_data.

sample_names-methods: Get sample names.

sample_sums: Returns the total number of individuals observed from each...

sample_variables: Get the sample variables present in sample_data

show-methods: method extensions to show for phyloseq objects.

show_mothur_cutoffs: Show cutoff values available in a mothur file.

splat.phyloseq.objects: Convert 'phyloseq-class' into a named list of its non-empty...

subset_ord_plot: Subset points from an ordination-derived ggplot

subset_samples-methods: Subset samples by sample_data expression

subset_taxa-methods: Subset species by taxonomic expression

taxa_are_rows-methods: Access taxa_are_rows slot from otu_table objects.

taxa_names-methods: Get species / taxa names.

taxa_sums: Returns the total number of individuals observed from each...

tax_glom: Agglomerate taxa of the same type.

taxonomyTable-class: An S4 class that holds taxonomic classification data as a...

tax_table-methods: Build or access the taxonomyTable.

threshrank: Thresholded rank transformation.

threshrankfun: A closure version of the 'threshrank' function.

tip_glom: Agglomerate closely-related taxa using single-linkage...

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

topk: Make filter fun. the most abundant 'k' taxa

topp: Make filter fun. that returns the most abundant 'p' fraction...

transformcounts: Transform abundance data in an 'otu_table', sample-by-sample.

transpose-methods: Transpose 'otu_table-class' or 'phyloseq-class'

tree_layout: Returns a data table defining the line segments of a...

UniFrac-methods: Calculate weighted or unweighted (Fast) UniFrac distance for...

Files in this package

phyloseq/DESCRIPTION
phyloseq/NAMESPACE
phyloseq/R
phyloseq/R/IO-methods.R phyloseq/R/allClasses.R phyloseq/R/allData.R phyloseq/R/allPackage.R phyloseq/R/almostAllAccessors.R phyloseq/R/as-methods.R phyloseq/R/assignment-methods.R phyloseq/R/deprecated_functions.R phyloseq/R/distance-methods.R phyloseq/R/extend_DESeq2.R phyloseq/R/extend_metagenomeSeq.R phyloseq/R/extend_vegan.R phyloseq/R/extract-methods.R phyloseq/R/merge-methods.R phyloseq/R/multtest-wrapper.R phyloseq/R/network-methods.R phyloseq/R/ordination-methods.R phyloseq/R/otuTable-class.R phyloseq/R/phylo-class.R phyloseq/R/phyloseq-class.R phyloseq/R/plot-methods.R phyloseq/R/sampleData-class.R phyloseq/R/show-methods.R phyloseq/R/taxonomyTable-class.R phyloseq/R/transform_filter-methods.R phyloseq/R/validity-methods.R
phyloseq/README.html
phyloseq/README.md
phyloseq/TODO.txt
phyloseq/build
phyloseq/build/vignette.rds
phyloseq/data
phyloseq/data/GlobalPatterns.RData
phyloseq/data/datalist
phyloseq/data/enterotype.RData
phyloseq/data/esophagus.RData
phyloseq/data/soilrep.RData
phyloseq/inst
phyloseq/inst/CITATION
phyloseq/inst/NEWS
phyloseq/inst/doc
phyloseq/inst/doc/Unweighted_UniFrac.RData
phyloseq/inst/doc/phyloseq-FAQ.R
phyloseq/inst/doc/phyloseq-FAQ.Rmd
phyloseq/inst/doc/phyloseq-FAQ.html
phyloseq/inst/doc/phyloseq-analysis.R
phyloseq/inst/doc/phyloseq-analysis.Rmd
phyloseq/inst/doc/phyloseq-analysis.html
phyloseq/inst/doc/phyloseq-basics.R
phyloseq/inst/doc/phyloseq-basics.Rmd
phyloseq/inst/doc/phyloseq-basics.html
phyloseq/inst/doc/phyloseq-mixture-models.R
phyloseq/inst/doc/phyloseq-mixture-models.Rmd
phyloseq/inst/doc/phyloseq-mixture-models.html
phyloseq/inst/extdata
phyloseq/inst/extdata/GP_otu_table_rand_short.txt.gz
phyloseq/inst/extdata/GP_tree_rand_short.newick.gz
phyloseq/inst/extdata/biom-refseq.fasta
phyloseq/inst/extdata/biom-tree.phy
phyloseq/inst/extdata/esophagus.fn.list.gz
phyloseq/inst/extdata/esophagus.fn.shared.gz
phyloseq/inst/extdata/esophagus.good.groups.gz
phyloseq/inst/extdata/esophagus.tree.gz
phyloseq/inst/extdata/gg13-5-73.tree.gz
phyloseq/inst/extdata/gp500-pycogent.py
phyloseq/inst/extdata/gp500-uuf.csv
phyloseq/inst/extdata/gp500-wuf.csv
phyloseq/inst/extdata/gp500-wufu.csv
phyloseq/inst/extdata/gp500test.env.txt
phyloseq/inst/extdata/gp500test.tree
phyloseq/inst/extdata/master_map.txt
phyloseq/inst/extdata/min_dense_otu_table.biom
phyloseq/inst/extdata/min_sparse_otu_table.biom
phyloseq/inst/extdata/mothur_example.cons.taxonomy.gz
phyloseq/inst/extdata/qiime500-refseq.fasta
phyloseq/inst/extdata/rformat_dist_0.03.txt.gz
phyloseq/inst/extdata/rich_dense_otu_table.biom
phyloseq/inst/extdata/rich_sparse_otu_table.biom
phyloseq/inst/extdata/study_1457_split_library_seqs_and_mapping.zip
phyloseq/inst/extdata/study_816_split_library_seqs_and_mapping.tar.gz
phyloseq/inst/extdata/study_816_split_library_seqs_and_mapping.zip
phyloseq/inst/extdata/study_gp.txt
phyloseq/inst/extdata/usearch.uc
phyloseq/inst/scripts
phyloseq/inst/scripts/installer.R
phyloseq/man
phyloseq/man/DPCoA.Rd phyloseq/man/JSD.Rd phyloseq/man/UniFrac-methods.Rd phyloseq/man/access.Rd phyloseq/man/assign-otu_table.Rd phyloseq/man/assign-phy_tree.Rd phyloseq/man/assign-sample_data.Rd phyloseq/man/assign-sample_names.Rd phyloseq/man/assign-tax_table.Rd phyloseq/man/assign-taxa_are_rows.Rd phyloseq/man/assign-taxa_names.Rd phyloseq/man/build_tax_table.Rd phyloseq/man/capscale-phyloseq-methods.Rd phyloseq/man/cca-rda-phyloseq-methods.Rd phyloseq/man/chunkReOrder.Rd phyloseq/man/data-GlobalPatterns.Rd phyloseq/man/data-enterotype.Rd phyloseq/man/data-esophagus.Rd phyloseq/man/data-soilrep.Rd phyloseq/man/decorana.Rd phyloseq/man/dist-class.Rd phyloseq/man/distance.Rd phyloseq/man/distanceMethodList.Rd phyloseq/man/envHash2otu_table.Rd phyloseq/man/estimate_richness.Rd phyloseq/man/export_env_file.Rd phyloseq/man/export_mothur_dist.Rd phyloseq/man/extract-methods.Rd phyloseq/man/filter_taxa.Rd phyloseq/man/filterfun_sample.Rd phyloseq/man/fix_phylo.Rd phyloseq/man/gapstat_ord.Rd phyloseq/man/genefilter_sample-methods.Rd phyloseq/man/get.component.classes.Rd phyloseq/man/get_sample-methods.Rd phyloseq/man/get_taxa-methods.Rd phyloseq/man/get_taxa_unique.Rd phyloseq/man/get_variable.Rd phyloseq/man/getslots.phyloseq.Rd phyloseq/man/import.Rd phyloseq/man/import_RDP_cluster.Rd phyloseq/man/import_RDP_otu.Rd phyloseq/man/import_biom.Rd phyloseq/man/import_env_file.Rd phyloseq/man/import_mothur.Rd phyloseq/man/import_mothur_constaxonomy.Rd phyloseq/man/import_mothur_dist.Rd phyloseq/man/import_mothur_groups.Rd phyloseq/man/import_mothur_otu_table.Rd phyloseq/man/import_mothur_otulist.Rd phyloseq/man/import_mothur_shared.Rd phyloseq/man/import_pyrotagger_tab.Rd phyloseq/man/import_qiime.Rd phyloseq/man/import_qiime_otu_tax.Rd phyloseq/man/import_qiime_sample_data.Rd phyloseq/man/import_uparse.Rd phyloseq/man/import_usearch_uc.Rd phyloseq/man/index_reorder.Rd phyloseq/man/intersect_taxa.Rd phyloseq/man/make_network.Rd phyloseq/man/merge_phyloseq.Rd phyloseq/man/merge_phyloseq_pair-methods.Rd phyloseq/man/merge_samples-methods.Rd phyloseq/man/merge_taxa-methods.Rd phyloseq/man/metaMDS.Rd phyloseq/man/microbio_me_qiime.Rd phyloseq/man/mt-methods.Rd phyloseq/man/nodeplotblank.Rd phyloseq/man/nodeplotboot.Rd phyloseq/man/nodeplotdefault.Rd phyloseq/man/nsamples-methods.Rd phyloseq/man/ntaxa-methods.Rd phyloseq/man/ordinate.Rd phyloseq/man/otu_table-class.Rd phyloseq/man/otu_table-methods.Rd phyloseq/man/parseTaxonomy-functions.Rd phyloseq/man/pcoa.Rd phyloseq/man/phy_tree-methods.Rd phyloseq/man/phylo-class.Rd phyloseq/man/phylo.Rd phyloseq/man/phyloseq-class.Rd phyloseq/man/phyloseq-deprecated.Rd phyloseq/man/phyloseq-package.Rd phyloseq/man/phyloseq.Rd phyloseq/man/phyloseq_to_deseq2.Rd phyloseq/man/phyloseq_to_metagenomeSeq.Rd phyloseq/man/plot_bar.Rd phyloseq/man/plot_clusgap.Rd phyloseq/man/plot_heatmap.Rd phyloseq/man/plot_net.Rd phyloseq/man/plot_network.Rd phyloseq/man/plot_ordination.Rd phyloseq/man/plot_phyloseq-methods.Rd phyloseq/man/plot_richness.Rd phyloseq/man/plot_scree.Rd phyloseq/man/plot_tree.Rd phyloseq/man/prune_samples-methods.Rd phyloseq/man/prune_taxa-methods.Rd phyloseq/man/psmelt.Rd phyloseq/man/rank_names.Rd phyloseq/man/rarefy_even_depth.Rd phyloseq/man/read_tree.Rd phyloseq/man/read_tree_greengenes.Rd phyloseq/man/reconcile_categories.Rd phyloseq/man/refseq-methods.Rd phyloseq/man/rm_outlierf.Rd phyloseq/man/sample_data-class.Rd phyloseq/man/sample_data-methods.Rd phyloseq/man/sample_names-methods.Rd phyloseq/man/sample_sums.Rd phyloseq/man/sample_variables.Rd phyloseq/man/show-methods.Rd phyloseq/man/show_mothur_cutoffs.Rd phyloseq/man/splat.phyloseq.objects.Rd phyloseq/man/subset_ord_plot.Rd phyloseq/man/subset_samples-methods.Rd phyloseq/man/subset_taxa-methods.Rd phyloseq/man/tax_glom.Rd phyloseq/man/tax_table-methods.Rd phyloseq/man/taxa_are_rows-methods.Rd phyloseq/man/taxa_names-methods.Rd phyloseq/man/taxa_sums.Rd phyloseq/man/taxonomyTable-class.Rd phyloseq/man/threshrank.Rd phyloseq/man/threshrankfun.Rd phyloseq/man/tip_glom.Rd phyloseq/man/topf.Rd phyloseq/man/topk.Rd phyloseq/man/topp.Rd phyloseq/man/transformcounts.Rd phyloseq/man/transpose-methods.Rd phyloseq/man/tree_layout.Rd
phyloseq/tests
phyloseq/tests/testthat
phyloseq/tests/testthat-phyloseq.R
phyloseq/tests/testthat/test-IO.R
phyloseq/tests/testthat/test-distance.R
phyloseq/tests/testthat/test-merge.R
phyloseq/tests/testthat/test-phyloseq.R
phyloseq/tests/testthat/test-plot.R
phyloseq/tests/testthat/test-rarefy.R
phyloseq/tests/testthat/test-subset.R
phyloseq/tests/testthat/test-transform.R
phyloseq/vignettes
phyloseq/vignettes/import_qiime_directory_structure.jpg
phyloseq/vignettes/phyloseq-FAQ.Rmd
phyloseq/vignettes/phyloseq-analysis.Rmd
phyloseq/vignettes/phyloseq-basics.Rmd
phyloseq/vignettes/phyloseq-mixture-models.Rmd
phyloseq/vignettes/phyloseq_classes_7.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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