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