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phyloseq (version 1.16.2)

Handling and analysis of high-throughput microbiome census data

Description

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

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Version

Version

1.16.2

License

AGPL-3

Maintainer

Paul McMurdie

Last Published

February 15th, 2017

Functions in phyloseq (1.16.2)

import_mothur_constaxonomy

Import mothur constaxonomy file and return a taxonomyTable

plot_ordination

General ordination plotter based on ggplot2.

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.

Assign a (new) phylogenetic tree to x

Prune unwanted OTUs / taxa from a phylogenetic object.

Get sample names.

General ordination eigenvalue plotter using ggplot2.

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.

A flexible, informative barplot phyloseq data

Import phyloseq data from biom-format file

Universal import method (wrapper) for phyloseq-package

Perform an ordination on phyloseq data

estimate_richness

Summarize alpha diversity

(Data) Reproducibility of soil microbiome data (2011)

A closure version of the threshrank function.

Thresholded rank transformation.

Agglomerate closely-related taxa using single-linkage clustering.

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)

Create an ecologically-organized heatmap using ggplot2 graphics

Force index order of phyloseq objects

Melt phyloseq data object into large data.frame

filterfun_sample

A sample-wise filter function builder analogous to filterfun.

Agglomerate taxa of the same type.

Plot a phylogenetic tree with optional annotations

read_tree_greengenes

Read GreenGenes tree released in annotated newick format

Returns the total number of individuals observed from each sample.

Estimate the gap statistic on an ordination result

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.

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

Universal slot accessor function for phyloseq-class.

Method for fixing problems with phylo-class trees in phyloseq

genefilter_sample

Filter OTUs with arbitrary function, sample-wise.

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

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

S3 class placeholder definition (list) for metaMDS

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.

S3 class placeholder definition (list) for phylogenetic trees.

phyloseq-deprecated

Depcrecated functions in the phyloseq package.

Generic plot defaults for phyloseq.

[,otu_table,ANY,ANY,ANY-method

Method extensions to extraction operator for phyloseq objects.

Build or access the otu_table.

reconcile_categories

Cleans absent levels in sample_data/data.frame.

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.

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

nodeplotdefault

Generates a default node-label function

Retrieve the names of the taxonomic ranks

Get species / taxa names.

transform_sample_counts

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

Replace OTU identifier names

Transpose otu_table-class or phyloseq-class

Get the values for a particular variable in sample_data

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

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 microbiome network (igraph)

The main experiment-level class for phyloseq data

Replace OTU identifier names

import_mothur_shared

Import mothur shared file and return an otu_table

Somewhat flexible tree-import function

sample_variables

Get the sample variables present in sample_data

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

Build or access sample_data.

splat.phyloseq.objects

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

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

Calculate the Jensen-Shannon Divergence (distance)

Constrained Correspondence Analysis and Redundancy Analysis.

Calculate distance, dissimilarity

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 arguments into one phyloseq object.

Build phyloseq-class objects from their components.

Create a ggplot summary of gap statistic results

Multiple testing of taxa abundance according to sample categories/classes

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

Get the number of taxa/species.

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

distanceMethodList

List of distance method keys supported in distance

An S4 placeholder for the dist class.

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 http://www.drive5.com/usearch/manual/opt_uparseout.html{UPARSE file format}

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

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

Function to avoid plotting node labels

Get the number of samples.

S3 class for ape-calculated MDS results

subset_ord_plot

Subset points from an ordination-derived ggplot

Make filter fun. the most abundant k taxa

parse_taxonomy_default

Parse elements of a taxonomy vector

Assign (new) sample_data to x

S3 class placeholder definition (list) for decorana

get.component.classes

Show the component objects classes and slot names.

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

Subset species by taxonomic expression

import_RDP_cluster

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

Build or access the taxonomyTable.

General function for importing mothur data files into phyloseq.

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

Assign a new OTU Table to x

export_mothur_dist

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

Calculate Double Principle Coordinate Analysis (DPCoA) using phylogenetic distance

import_env_file

Read a UniFrac-formatted ENV file.

Returns all abundance values of sample i.

Merge samples based on a sample variable or factor.

import_usearch_uc

Import usearch table format (.uc) to OTU table

Retrieve phylogenetic tree (phylo-class) from object.

phyloseq_to_deseq2

Convert phyloseq data to DESeq2 dds object

Microbiome Network Plot using ggplot2