phyloseq v1.16.2

by Paul McMurdie

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.

Functions in phyloseq

Name Description
import_mothur_constaxonomy Import mothur constaxonomy file and return a taxonomyTable
plot_ordination General ordination plotter based on ggplot2.
plot_network Microbiome Network Plot using ggplot2
rarefy_even_depth Resample an OTU table such that all samples have the same library size.
phyloseq_to_metagenomeSeq Convert phyloseq data to MetagenomeSeq MRexperiment object
taxa_are_rows<- Manually change taxa_are_rows through assignment.
phy_tree<- Assign a (new) phylogenetic tree to x
prune_taxa Prune unwanted OTUs / taxa from a phylogenetic object.
sample_names Get sample names.
plot_scree General ordination eigenvalue plotter using ggplot2.
subset_samples Subset samples by sample_data expression
export_env_file Export environment (ENV) file for UniFrac Server.
envHash2otu_table Convert a sequence-sample hash (like ENV file) into an OTU table.
plot_bar A flexible, informative barplot phyloseq data
import_biom Import phyloseq data from biom-format file
import Universal import method (wrapper) for phyloseq-package
ordinate Perform an ordination on phyloseq data
estimate_richness Summarize alpha diversity
data-soilrep (Data) Reproducibility of soil microbiome data (2011)
threshrankfun A closure version of the threshrank function.
threshrank Thresholded rank transformation.
tip_glom Agglomerate closely-related taxa using single-linkage clustering.
tax_table<- Assign a (new) Taxonomy Table to x
import_pyrotagger_tab Imports a tab-delimited version of the pyrotagger output file.
data-enterotype (Data) Enterotypes of the human gut microbiome (2011)
plot_heatmap Create an ecologically-organized heatmap using ggplot2 graphics
index_reorder Force index order of phyloseq objects
psmelt Melt phyloseq data object into large data.frame
filterfun_sample A sample-wise filter function builder analogous to filterfun.
tax_glom Agglomerate taxa of the same type.
plot_tree Plot a phylogenetic tree with optional annotations
read_tree_greengenes Read GreenGenes tree released in annotated newick format
sample_sums Returns the total number of individuals observed from each sample.
gapstat_ord Estimate the gap statistic on an ordination result
get_sample Returns all abundance values for species i.
getslots.phyloseq Return the non-empty slot names of a phyloseq object.
taxonomyTable-class An S4 class that holds taxonomic classification data as a character matrix.
topf Make filter fun. that returns the top f fraction of taxa in a sample.
import_mothur_otu_table Import mothur list and group files and return an otu_table
access Universal slot accessor function for phyloseq-class.
fix_phylo Method for fixing problems with phylo-class trees in phyloseq
genefilter_sample Filter OTUs with arbitrary function, sample-wise.
filter_taxa Filter taxa based on across-sample OTU abundance criteria
otu_table-class The S4 class for storing taxa-abundance information.
import_mothur_dist Import mothur-formatted distance file
phylo-class An S4 placeholder of the main phylogenetic tree class from the ape package.
metaMDS S3 class placeholder definition (list) for metaMDS
import_RDP_otu Import new RDP OTU-table format
data-GlobalPatterns (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)
build_tax_table Build a tax_table from a named possibly-jagged list
import_qiime_sample_data Import just sample_data file from QIIME pipeline.
phylo S3 class placeholder definition (list) for phylogenetic trees.
phyloseq-deprecated Depcrecated functions in the phyloseq package.
plot_phyloseq Generic plot defaults for phyloseq.
[,otu_table,ANY,ANY,ANY-method Method extensions to extraction operator for phyloseq objects.
otu_table Build or access the otu_table.
reconcile_categories Cleans absent levels in sample_data/data.frame.
plot_richness Plot alpha diversity, flexibly with ggplot2
phyloseq-package Handling and analysis of high-throughput phylogenetic sequence data.
show_mothur_cutoffs Show cutoff values available in a mothur file.
taxa_are_rows Access taxa_are_rows slot from otu_table objects.
capscale.phyloseq Constrained Analysis of Principal Coordinates, capscale.
sample_data-class The S4 for storing sample variables.
get_taxa_unique Get a unique vector of the observed taxa at a particular taxonomic rank
merge_taxa Merge a subset of the species in x into one species/taxa/OTU.
nodeplotdefault Generates a default node-label function
rank_names Retrieve the names of the taxonomic ranks
taxa_names Get species / taxa names.
transform_sample_counts Transform abundance data in an otu_table, sample-by-sample.
sample_names<- Replace OTU identifier names
t Transpose otu_table-class or phyloseq-class
get_variable Get the values for a particular variable in sample_data
prune_samples Define a subset of samples to keep in a phyloseq object.
refseq Retrieve reference sequences (XStringSet-class) from object.
show,otu_table-method method extensions to show for phyloseq objects.
import_mothur_groups Parse mothur group file into a simple hash table.
make_network Make microbiome network (igraph)
phyloseq-class The main experiment-level class for phyloseq data
taxa_names<- Replace OTU identifier names
import_mothur_shared Import mothur shared file and return an otu_table
read_tree Somewhat flexible tree-import function
sample_variables Get the sample variables present in sample_data
rm_outlierf Set to FALSE any outlier species greater than f fractional abundance.
sample_data Build or access sample_data.
splat.phyloseq.objects Convert phyloseq-class into a named list of its non-empty components.
topp Make filter fun. that returns the most abundant p fraction of taxa
JSD Calculate the Jensen-Shannon Divergence (distance)
cca.phyloseq Constrained Correspondence Analysis and Redundancy Analysis.
distance Calculate distance, dissimilarity
chunkReOrder Chunk re-order a vector so that specified newstart is first.
import_qiime_otu_tax Import now legacy-format QIIME OTU table as a list of two matrices.
merge_phyloseq Merge arguments into one phyloseq object.
phyloseq Build phyloseq-class objects from their components.
plot_clusgap Create a ggplot summary of gap statistic results
mt Multiple testing of taxa abundance according to sample categories/classes
tree_layout Returns a data table defining the line segments of a phylogenetic tree.
ntaxa Get the number of taxa/species.
UniFrac Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs.
distanceMethodList List of distance method keys supported in distance
dist-class An S4 placeholder for the dist class.
import_qiime Import function to read the now legacy-format QIIME OTU table.
import_mothur_otulist Import mothur list file and return as list object in R.
import_uparse Import http://www.drive5.com/usearch/manual/opt_uparseout.html{UPARSE file format}
intersect_taxa Returns the intersection of species and samples for the components of x
merge_phyloseq_pair Merge pair of phyloseq component data objects of the same class.
microbio_me_qiime Import microbio.me/qiime (QIIME-DB) data package
nodeplotboot Generates a function for labeling bootstrap values on a phylogenetic tree.
nodeplotblank Function to avoid plotting node labels
nsamples Get the number of samples.
pcoa S3 class for ape-calculated MDS results
subset_ord_plot Subset points from an ordination-derived ggplot
topk Make filter fun. the most abundant k taxa
parse_taxonomy_default Parse elements of a taxonomy vector
sample_data<- Assign (new) sample_data to x
decorana S3 class placeholder definition (list) for decorana
get.component.classes Show the component objects classes and slot names.
data-esophagus (Data) Small example dataset from a human esophageal community (2004)
subset_taxa Subset species by taxonomic expression
import_RDP_cluster Import RDP cluster file and return otu_table (abundance table).
tax_table Build or access the taxonomyTable.
import_mothur General function for importing mothur data files into phyloseq.
taxa_sums Returns the total number of individuals observed from each species/taxa/OTU.
otu_table<- Assign a new OTU Table to x
export_mothur_dist Export a distance object as .names and .dist files for mothur
DPCoA Calculate Double Principle Coordinate Analysis (DPCoA) using phylogenetic distance
import_env_file Read a UniFrac-formatted ENV file.
get_taxa Returns all abundance values of sample i.
merge_samples Merge samples based on a sample variable or factor.
import_usearch_uc Import usearch table format (.uc) to OTU table
phy_tree Retrieve phylogenetic tree (phylo-class) from object.
phyloseq_to_deseq2 Convert phyloseq data to DESeq2 dds object
plot_net Microbiome Network Plot using ggplot2
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Date 2016-04-16
License AGPL-3
VignetteBuilder knitr
biocViews Sequencing, Microbiome, Metagenomics, Clustering, Classification, MultipleComparison, GeneticVariability
URL http://dx.plos.org/10.1371/journal.pone.0061217
BugReports https://github.com/joey711/phyloseq/issues
Collate 'allClasses.R' 'allPackage.R' 'allData.R' 'as-methods.R' 'show-methods.R' 'plot-methods.R' 'extract-methods.R' 'almostAllAccessors.R' 'otuTable-class.R' 'phyloseq-class.R' 'taxonomyTable-class.R' 'IO-methods.R' 'merge-methods.R' 'multtest-wrapper.R' 'ordination-methods.R' 'transform_filter-methods.R' 'validity-methods.R' 'assignment-methods.R' 'sampleData-class.R' 'extend_vegan.R' 'network-methods.R' 'distance-methods.R' 'deprecated_functions.R' 'extend_DESeq2.R' 'phylo-class.R' 'extend_metagenomeSeq.R'
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