Package: phyloseq 1.49.0
Paul J. McMurdie
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.
Authors:
phyloseq_1.49.0.tar.gz
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phyloseq.pdf |phyloseq.html✨
phyloseq/json (API)
NEWS
| # Install 'phyloseq' in R: |
| install.packages('phyloseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/joey711/phyloseq/issues
- GlobalPatterns -
- enterotype -
- esophagus -
- soilrep -
On BioConductor:phyloseq-1.49.0(bioc 3.20)phyloseq-1.48.0(bioc 3.19)
Last updated 2 months agofrom:6bb7e902cc
Exports:accessbuild_tax_tabledistancedistanceMethodListDPCoAestimate_richnessexport_env_fileexport_mothur_distfilter_taxafilterfun_samplefilterfunSamplegapstat_ordgenefilter_samplegenefilterSampleget_sampleget_taxaget_taxa_uniqueget_variablegetSamplesgetslots.phyloseqgetSpeciesgetTaxagetVariableimportimport_biomimport_env_fileimport_mothurimport_mothur_distimport_pyrotagger_tabimport_qiimeimport_qiime_otu_taximport_qiime_sample_dataimport_qiime_sampleDataimport_RDP_clusterimport_RDP_otuimport_uparseimport_usearch_ucmake_networkmerge_phyloseqmerge_phyloseq_pairmerge_samplesmerge_speciesmerge_taxamicrobio_me_qiimemtnodeplotblanknodeplotbootnodeplotdefaultnsamplesnspeciesntaxaordinateotu_tableotu_table<-otuTableotuTable<-parse_taxonomy_defaultparse_taxonomy_greengenesparse_taxonomy_qiimephy_treephy_tree<-phyloseqphyloseq_to_deseq2phyloseq_to_metagenomeSeqplot_barplot_clusgapplot_heatmapplot_netplot_networkplot_ordinationplot_phyloseqplot_richnessplot_richness_estimatesplot_screeplot_taxa_barplot_treeprune_samplesprune_speciesprune_taxapsmeltrank_namesrank.namesrarefy_even_depthread_treeread_tree_greengenesrefseqrm_outlierfsam_datasam_data<-samDatasample_datasample_data<-sample_namessample_names<-sample_sumssample_variablessample.namessample.variablessampleDatasampleData<-sampleNamessampleSumsshowshow_mothur_cutoffsshow_mothur_list_cutoffsspecies.namesspeciesarerowsspeciesAreRowsspeciesAreRows<-speciesSumssubset_ord_plotsubset_samplessubset_speciessubset_taxattax_glomtax_tabletax_table<-taxa_are_rowstaxa_are_rows<-taxa_namestaxa_names<-taxa_sumstaxaplottaxglomtaxtabtaxTabtaxTab<-threshrankthreshrankfuntip_glomtipglomtopftopktopptransform_sample_countstransformSampleCountstretre<-tree_layoutUniFrac
Dependencies:ade4apeaskpassBiobaseBiocGenericsbiomformatBiostringscliclustercodetoolscolorspacecpp11crayoncurldata.tabledigestfansifarverforeachGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemulttestmunsellnlmeopensslpermutepillarpixmappkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5librlangS4VectorsscalesspstringistringrsurvivalsystibbleUCSC.utilsutf8vctrsveganviridisLitewithrXVectorzlibbioc
analysis vignette
Rendered fromphyloseq-analysis.Rmdusingknitr::rmarkdownon May 27 2024.Last update: 2018-07-15
Started: 2013-10-16
phyloseq and DESeq2 on Colorectal Cancer Data
Rendered fromphyloseq-mixture-models.Rmdusingknitr::rmarkdownon May 27 2024.Last update: 2016-12-12
Started: 2013-10-24
phyloseq basics vignette
Rendered fromphyloseq-basics.Rmdusingknitr::rmarkdownon May 27 2024.Last update: 2016-03-21
Started: 2013-10-16
phyloseq Frequently Asked Questions (FAQ)
Rendered fromphyloseq-FAQ.Rmdusingknitr::rmarkdownon May 27 2024.Last update: 2019-02-17
Started: 2016-03-23
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Handling and analysis of high-throughput phylogenetic sequence data. | phyloseq-package |
| Method extensions to extraction operator for phyloseq objects. | [,otu_table,ANY,ANY,ANY-method [,sample_data,ANY,ANY,ANY-method [,taxonomyTable,ANY,ANY,ANY-method [,XStringSet,character,ANY,ANY-method |
| Universal slot accessor function for phyloseq-class. | access |
| Build a 'tax_table' from a named possibly-jagged list | build_tax_table |
| (Data) Enterotypes of the human gut microbiome (2011) | data-enterotype enterotype |
| (Data) Small example dataset from a human esophageal community (2004) | data-esophagus esophagus |
| (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011) | data-GlobalPatterns GlobalPatterns |
| (Data) Reproducibility of soil microbiome data (2011) | data-soilrep soilrep |
| An S4 placeholder for the 'dist' class. | dist-class |
| Calculate distance, dissimilarity | distance distance,otu_table,character-method distance,phyloseq,ANY-method distance,phyloseq,character-method |
| List of distance method keys supported in 'distance' | distanceMethodList |
| Calculate Double Principle Coordinate Analysis (DPCoA) using phylogenetic distance | DPCoA |
| Summarize alpha diversity | estimate_richness |
| Export environment (ENV) file for UniFrac Server. | export_env_file |
| Export a distance object as '.names' and '.dist' files for mothur | export_mothur_dist |
| Filter taxa based on across-sample OTU abundance criteria | filter_taxa |
| A sample-wise filter function builder analogous to 'filterfun'. | filterfun_sample |
| Estimate the gap statistic on an ordination result | gapstat_ord |
| Filter OTUs with arbitrary function, sample-wise. | genefilter_sample genefilter_sample,matrix-method genefilter_sample,otu_table-method genefilter_sample,phyloseq-method |
| Returns all abundance values for species 'i'. | get_sample get_sample,otu_table-method get_sample,phyloseq-method |
| Returns all abundance values of sample 'i'. | get_taxa get_taxa,otu_table-method get_taxa,phyloseq-method |
| Get a unique vector of the observed taxa at a particular taxonomic rank | get_taxa_unique |
| Get the values for a particular variable in sample_data | get_variable |
| Return the non-empty slot names of a phyloseq object. | getslots.phyloseq |
| Universal import method (wrapper) for phyloseq-package | import |
| Import phyloseq data from biom-format file | import_biom |
| Read a UniFrac-formatted ENV file. | import_env_file |
| General function for importing mothur data files into phyloseq. | import_mothur |
| Import mothur-formatted distance file | import_mothur_dist |
| Imports a tab-delimited version of the pyrotagger output file. | import_pyrotagger_tab |
| Import function to read the now legacy-format QIIME OTU table. | import_qiime |
| Import now legacy-format QIIME OTU table as a list of two matrices. | import_qiime_otu_tax |
| Import just 'sample_data' file from QIIME pipeline. | import_qiime_sample_data |
| Import RDP cluster file and return otu_table (abundance table). | import_RDP_cluster |
| Import new RDP OTU-table format | import_RDP_otu |
| Import UPARSE file format | import_uparse |
| Import usearch table format ('.uc') to OTU table | import_usearch_uc |
| Make microbiome network (igraph) | make_network |
| Merge arguments into one phyloseq object. | merge_phyloseq |
| Merge pair of phyloseq component data objects of the same class. | merge_phyloseq_pair merge_phyloseq_pair,otu_table,otu_table-method merge_phyloseq_pair,phylo,phylo-method merge_phyloseq_pair,sample_data,sample_data-method merge_phyloseq_pair,taxonomyTable,taxonomyTable-method merge_phyloseq_pair,XStringSet,XStringSet-method |
| Merge samples based on a sample variable or factor. | merge_samples merge_samples,otu_table-method merge_samples,phyloseq-method merge_samples,sample_data-method |
| Merge a subset of the species in 'x' into one species/taxa/OTU. | merge_taxa merge_taxa,otu_table-method merge_taxa,phylo-method merge_taxa,phyloseq-method merge_taxa,sample_data-method merge_taxa,taxonomyTable-method merge_taxa,XStringSet-method |
| Import microbio.me/qiime (QIIME-DB) data package | microbio_me_qiime |
| Multiple testing of taxa abundance according to sample categories/classes | mt mt,otu_table,character-method mt,otu_table,factor-method mt,otu_table,integer-method mt,otu_table,logical-method mt,otu_table,numeric-method mt,phyloseq,ANY-method |
| Function to avoid plotting node labels | nodeplotblank |
| Generates a function for labeling bootstrap values on a phylogenetic tree. | nodeplotboot |
| Generates a default node-label function | nodeplotdefault |
| Get the number of samples. | nsamples nsamples,ANY-method nsamples,otu_table-method nsamples,phyloseq-method nsamples,sample_data-method |
| Get the number of taxa/species. | ntaxa ntaxa,ANY-method ntaxa,otu_table-method ntaxa,phylo-method ntaxa,phyloseq-method ntaxa,taxonomyTable-method ntaxa,XStringSet-method |
| Perform an ordination on phyloseq data | ordinate |
| Build or access the otu_table. | otu_table otu_table,ANY-method otu_table,data.frame-method otu_table,matrix-method otu_table,otu_table-method otu_table,phyloseq-method |
| The S4 class for storing taxa-abundance information. | otu_table-class |
| Assign a new OTU Table to 'x' | assign-otu_table otu_table<- otu_table<-,otu_table,otu_table-method otu_table<-,phyloseq,otu_table-method otu_table<-,phyloseq,phyloseq-method |
| Parse elements of a taxonomy vector | parse_taxonomy_default parse_taxonomy_greengenes parse_taxonomy_qiime |
| Retrieve phylogenetic tree ('phylo'-class) from object. | phy_tree phy_tree,ANY-method phy_tree,phylo-method |
| Assign a (new) phylogenetic tree to 'x' | assign-phy_tree phy_tree<- phy_tree<-,phyloseq,phylo-method phy_tree<-,phyloseq,phyloseq-method |
| An S4 placeholder of the main phylogenetic tree class from the ape package. | phylo-class |
| Build phyloseq-class objects from their components. | phyloseq |
| Convert phyloseq data to DESeq2 dds object | phyloseq_to_deseq2 |
| Convert phyloseq data to MetagenomeSeq MRexperiment object | phyloseq_to_metagenomeSeq |
| The main experiment-level class for phyloseq data | phyloseq-class |
| Depcrecated functions in the phyloseq package. | phyloseq-deprecated-package deprecated_phyloseq_function filterfunSample genefilterSample getSamples getSpecies getTaxa getVariable import_qiime_sampleData merge_species nspecies otuTable otuTable<- phyloseq-deprecated plot_richness_estimates plot_taxa_bar prune_species rank.names samData sample.names sample.variables sampleData sampleData<- sampleNames sampleSums sam_data sam_data<- show_mothur_list_cutoffs species.names speciesAreRows speciesarerows speciesAreRows<- speciesSums subset_species taxaplot taxglom taxTab taxtab taxTab<- tipglom tre tre<- |
| A flexible, informative barplot phyloseq data | plot_bar |
| Create a ggplot summary of gap statistic results | plot_clusgap |
| Create an ecologically-organized heatmap using ggplot2 graphics | plot_heatmap |
| Microbiome Network Plot using ggplot2 | plot_net |
| Microbiome Network Plot using ggplot2 | plot_network |
| General ordination plotter based on ggplot2. | plot_ordination |
| Generic plot defaults for phyloseq. | plot_phyloseq plot_phyloseq,phyloseq-method |
| Plot alpha diversity, flexibly with ggplot2 | plot_richness |
| General ordination eigenvalue plotter using ggplot2. | plot_scree |
| Plot a phylogenetic tree with optional annotations | plot_tree |
| Define a subset of samples to keep in a phyloseq object. | prune_samples prune_samples,character,otu_table-method prune_samples,character,phyloseq-method prune_samples,character,sample_data-method prune_samples,logical,ANY-method |
| Prune unwanted OTUs / taxa from a phylogenetic object. | prune_taxa prune_taxa,character,otu_table-method prune_taxa,character,phylo-method prune_taxa,character,phyloseq-method prune_taxa,character,sample_data-method prune_taxa,character,taxonomyTable-method prune_taxa,character,XStringSet-method prune_taxa,logical,ANY-method prune_taxa,NULL,ANY-method |
| Melt phyloseq data object into large data.frame | psmelt |
| Retrieve the names of the taxonomic ranks | rank_names |
| Resample an OTU table such that all samples have the same library size. | rarefy_even_depth |
| Somewhat flexible tree-import function | read_tree |
| Read GreenGenes tree released in annotated newick format | read_tree_greengenes |
| Retrieve reference sequences ('XStringSet'-class) from object. | refseq refseq,ANY-method refseq,XStringSet-method |
| Set to FALSE any outlier species greater than f fractional abundance. | rm_outlierf |
| Build or access sample_data. | sample_data sample_data,ANY-method sample_data,data.frame-method |
| The S4 for storing sample variables. | sample_data-class |
| Assign (new) sample_data to 'x' | assign-sample_data sample_data<- |
| Get sample names. | sample_names sample_names,ANY-method sample_names,otu_table-method sample_names,phyloseq-method sample_names,sample_data-method |
| Replace OTU identifier names | assign-sample_names sample_names<- sample_names<-,ANY,ANY-method sample_names<-,ANY,character-method sample_names<-,otu_table,character-method sample_names<-,phyloseq,character-method sample_names<-,sample_data,character-method |
| Returns the total number of individuals observed from each sample. | sample_sums |
| Get the sample variables present in sample_data | sample_variables |
| Show cutoff values available in a mothur file. | show_mothur_cutoffs |
| method extensions to show for phyloseq objects. | show,otu_table-method show,phyloseq-method show,sample_data-method show,taxonomyTable-method |
| Subset points from an ordination-derived ggplot | subset_ord_plot |
| Subset samples by sample_data expression | subset_samples |
| Subset species by taxonomic expression | subset_taxa |
| Transpose 'otu_table-class' or 'phyloseq-class' | t t,otu_table-method t,phyloseq-method |
| Agglomerate taxa of the same type. | tax_glom |
| Build or access the taxonomyTable. | tax_table tax_table,ANY-method tax_table,data.frame-method tax_table,matrix-method |
| Assign a (new) Taxonomy Table to 'x' | assign-tax_table tax_table<- tax_table<-,phyloseq,ANY-method tax_table<-,phyloseq,taxonomyTable-method tax_table<-,taxonomyTable,ANY-method tax_table<-,taxonomyTable,taxonomyTable-method |
| Access taxa_are_rows slot from otu_table objects. | taxa_are_rows taxa_are_rows,ANY-method taxa_are_rows,otu_table-method taxa_are_rows,phyloseq-method |
| Manually change taxa_are_rows through assignment. | assign-taxa_are_rows taxa_are_rows<- taxa_are_rows<-,otu_table,logical-method taxa_are_rows<-,phyloseq,logical-method |
| Get species / taxa names. | taxa_names taxa_names,ANY-method taxa_names,otu_table-method taxa_names,phylo-method taxa_names,phyloseq-method taxa_names,sample_data-method taxa_names,taxonomyTable-method taxa_names,XStringSet-method |
| Replace OTU identifier names | assign-taxa_names taxa_names<- taxa_names<-,ANY,ANY-method taxa_names<-,ANY,character-method taxa_names<-,otu_table,character-method taxa_names<-,phylo,character-method taxa_names<-,phyloseq,character-method taxa_names<-,taxonomyTable,character-method taxa_names<-,XStringSet,character-method |
| Returns the total number of individuals observed from each species/taxa/OTU. | taxa_sums |
| An S4 class that holds taxonomic classification data as a character matrix. | taxonomyTable-class |
| Thresholded rank transformation. | threshrank |
| A closure version of the 'threshrank' function. | threshrankfun |
| Agglomerate closely-related taxa using single-linkage clustering. | tip_glom |
| Make filter fun. that returns the top f fraction of taxa in a sample. | topf |
| Make filter fun. the most abundant 'k' taxa | topk |
| Make filter fun. that returns the most abundant 'p' fraction of taxa | topp |
| Transform abundance data in an 'otu_table', sample-by-sample. | transformSampleCounts transform_sample_counts |
| Returns a data table defining the line segments of a phylogenetic tree. | tree_layout |
| Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs. | UniFrac UniFrac,phyloseq-method |
