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

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

Author
Paul J. McMurdie <mcmurdie@stanford.edu>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain
Date of publication
None
Maintainer
Paul J. McMurdie <mcmurdie@stanford.edu>
License
AGPL-3
Version
1.18.1
URLs

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