Man pages for phyloseq
Handling and analysis of high-throughput microbiome census data

accessUniversal slot accessor function for phyloseq-class.
assign-otu_tableAssign a new OTU Table to 'x'
assign-phy_treeAssign a (new) phylogenetic tree to 'x'
assign-sample_dataAssign (new) sample_data to 'x'
assign-sample_namesReplace OTU identifier names
assign-taxa_are_rowsManually change taxa_are_rows through assignment.
assign-taxa_namesReplace OTU identifier names
assign-tax_tableAssign a (new) Taxonomy Table to 'x'
build_tax_tableBuild a 'tax_table' from a named possibly-jagged list
capscale-phyloseq-methodsConstrained Analysis of Principal Coordinates, 'capscale'.
cca-rda-phyloseq-methodsConstrained Correspondence Analysis and Redundancy Analysis.
chunkReOrderChunk 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)
decoranaS3 class placeholder definition (list) for decorana
distanceCalculate distance, dissimilarity
distanceMethodListList of distance method keys supported in 'distance'
dist-classAn S4 placeholder for the 'dist' class.
DPCoACalculate Double Principle Coordinate Analysis (DPCoA) using...
envHash2otu_tableConvert a sequence-sample hash (like ENV file) into an OTU...
estimate_richnessSummarize alpha diversity
export_env_fileExport environment (ENV) file for UniFrac Server.
export_mothur_distExport a distance object as '.names' and '.dist' files for...
extract-methodsMethod extensions to extraction operator for phyloseq...
filterfun_sampleA sample-wise filter function builder analogous to...
filter_taxaFilter taxa based on across-sample OTU abundance criteria
fix_phyloMethod for fixing problems with phylo-class trees in phyloseq
gapstat_ordEstimate the gap statistic on an ordination result
genefilter_sample-methodsFilter OTUs with arbitrary function, sample-wise.
get.component.classesShow the component objects classes and slot names.
get_sample-methodsReturns all abundance values for species 'i'.
getslots.phyloseqReturn the non-empty slot names of a phyloseq object.
get_taxa-methodsReturns all abundance values of sample 'i'.
get_taxa_uniqueGet a unique vector of the observed taxa at a particular...
get_variableGet the values for a particular variable in sample_data
importUniversal import method (wrapper) for phyloseq-package
import_biomImport phyloseq data from biom-format file
import_env_fileRead a UniFrac-formatted ENV file.
import_mothurGeneral function for importing mothur data files into...
import_mothur_constaxonomyImport mothur constaxonomy file and return a taxonomyTable
import_mothur_distImport mothur-formatted distance file
import_mothur_groupsParse mothur group file into a simple hash table.
import_mothur_otulistImport mothur list file and return as list object in R.
import_mothur_otu_tableImport mothur list and group files and return an otu_table
import_mothur_sharedImport mothur shared file and return an otu_table
import_pyrotagger_tabImports a tab-delimited version of the pyrotagger output...
import_qiimeImport function to read the now legacy-format QIIME OTU...
import_qiime_otu_taxImport now legacy-format QIIME OTU table as a list of two...
import_qiime_sample_dataImport just 'sample_data' file from QIIME pipeline.
import_RDP_clusterImport RDP cluster file and return otu_table (abundance...
import_RDP_otuImport new RDP OTU-table format
import_uparseImport UPARSE file format
import_usearch_ucImport usearch table format ('.uc') to OTU table
index_reorderForce index order of phyloseq objects
intersect_taxaReturns the intersection of species and samples for the...
JSDCalculate the Jensen-Shannon Divergence (distance)
make_networkMake microbiome network (igraph)
merge_phyloseqMerge arguments into one phyloseq object.
merge_phyloseq_pair-methodsMerge pair of phyloseq component data objects of the same...
merge_samples-methodsMerge samples based on a sample variable or factor.
merge_taxa-methodsMerge a subset of the species in 'x' into one...
metaMDSS3 class placeholder definition (list) for metaMDS
microbio_me_qiimeImport (QIIME-DB) data package
mt-methodsMultiple testing of taxa abundance according to sample...
nodeplotblankFunction to avoid plotting node labels
nodeplotbootGenerates a function for labeling bootstrap values on a...
nodeplotdefaultGenerates a default node-label function
nsamples-methodsGet the number of samples.
ntaxa-methodsGet the number of taxa/species.
ordinatePerform an ordination on phyloseq data
otu_table-classThe S4 class for storing taxa-abundance information.
otu_table-methodsBuild or access the otu_table.
parseTaxonomy-functionsParse elements of a taxonomy vector
pcoaS3 class for ape-calculated MDS results
phyloS3 class placeholder definition (list) for phylogenetic...
phylo-classAn S4 placeholder of the main phylogenetic tree class from...
phyloseqBuild phyloseq-class objects from their components.
phyloseq-classThe main experiment-level class for phyloseq data
phyloseq-deprecatedDepcrecated functions in the phyloseq package.
phyloseq-packageHandling and analysis of high-throughput phylogenetic...
phyloseq_to_deseq2Convert phyloseq data to DESeq2 dds object
phyloseq_to_metagenomeSeqConvert phyloseq data to MetagenomeSeq MRexperiment object
phy_tree-methodsRetrieve phylogenetic tree ('phylo'-class) from object.
plot_barA flexible, informative barplot phyloseq data
plot_clusgapCreate a ggplot summary of gap statistic results
plot_heatmapCreate an ecologically-organized heatmap using ggplot2...
plot_netMicrobiome Network Plot using ggplot2
plot_networkMicrobiome Network Plot using ggplot2
plot_ordinationGeneral ordination plotter based on ggplot2.
plot_phyloseq-methodsGeneric plot defaults for phyloseq.
plot_richnessPlot alpha diversity, flexibly with ggplot2
plot_screeGeneral ordination eigenvalue plotter using ggplot2.
plot_treePlot a phylogenetic tree with optional annotations
prune_samples-methodsDefine a subset of samples to keep in a phyloseq object.
prune_taxa-methodsPrune unwanted OTUs / taxa from a phylogenetic object.
psmeltMelt phyloseq data object into large data.frame
rank_namesRetrieve the names of the taxonomic ranks
rarefy_even_depthResample an OTU table such that all samples have the same...
read_treeSomewhat flexible tree-import function
read_tree_greengenesRead GreenGenes tree released in annotated newick format
reconcile_categoriesCleans absent levels in sample_data/data.frame.
refseq-methodsRetrieve reference sequences ('XStringSet'-class) from...
rm_outlierfSet to FALSE any outlier species greater than f fractional...
sample_data-classThe S4 for storing sample variables.
sample_data-methodsBuild or access sample_data.
sample_names-methodsGet sample names.
sample_sumsReturns the total number of individuals observed from each...
sample_variablesGet the sample variables present in sample_data
show-methodsmethod extensions to show for phyloseq objects.
show_mothur_cutoffsShow cutoff values available in a mothur file.
splat.phyloseq.objectsConvert 'phyloseq-class' into a named list of its non-empty...
subset_ord_plotSubset points from an ordination-derived ggplot
subset_samples-methodsSubset samples by sample_data expression
subset_taxa-methodsSubset species by taxonomic expression
taxa_are_rows-methodsAccess taxa_are_rows slot from otu_table objects.
taxa_names-methodsGet species / taxa names.
taxa_sumsReturns the total number of individuals observed from each...
tax_glomAgglomerate taxa of the same type.
taxonomyTable-classAn S4 class that holds taxonomic classification data as a...
tax_table-methodsBuild or access the taxonomyTable.
threshrankThresholded rank transformation.
threshrankfunA closure version of the 'threshrank' function.
tip_glomAgglomerate closely-related taxa using single-linkage...
topfMake filter fun. that returns the top f fraction of taxa in a...
topkMake filter fun. the most abundant 'k' taxa
toppMake filter fun. that returns the most abundant 'p' fraction...
transformcountsTransform abundance data in an 'otu_table', sample-by-sample.
transpose-methodsTranspose 'otu_table-class' or 'phyloseq-class'
tree_layoutReturns a data table defining the line segments of a...
UniFrac-methodsCalculate weighted or unweighted (Fast) UniFrac distance for...
phyloseq documentation built on Nov. 17, 2017, 8:33 a.m.