diff --git a/vignettes/phyloseq-basics.Rmd b/vignettes/phyloseq-basics.Rmd index a44421e9..f032f06d 100644 --- a/vignettes/phyloseq-basics.Rmd +++ b/vignettes/phyloseq-basics.Rmd @@ -168,11 +168,13 @@ One QIIME input file (sample map, tab-delimited), is recognized by the `import_qiime_sample_data()` function. --- + Input File(s) | phyloseq function | Output --- | --- | --- `.biom`, `.tre` | `import_biom()` | phyloseq object with OTU table, taxonomy table, and tree (if provided) `.tre` | `read_tree()` | `phylo` object, representing phylogenetic tree. `map.txt` | `import_qiime_sample_data()` | A `sample_data` object + --- The objects created by each of the import functions above @@ -317,6 +319,7 @@ Suppose you have already imported raw data from an experiment into `R`, and thei Table of component constructor functions for building component data objects --- + Function | Input Class | Output Description --- | --- | --- `otu_table` | numeric matrix | `otu_table` object storing OTU abundance @@ -326,15 +329,18 @@ Suppose you have already imported raw data from an experiment into `R`, and thei `tax_table` | data.frame | `taxonomyTable` object storing taxonomic identities `read_tree` | file path char | phylo-class tree, read from file `read.table` | table file path | A matrix or data.frame (Std `R` core function) + --- phyloseq constructors: functions for building/merging *phyloseq* objects. --- + Function | Input Class | Output Description --- | --- | --- `phyloseq` | Two or more component objects | phyloseq-class, *experiment-level* object `merge_phyloseq`| Two or more component or phyloseq-class objects | Combined instance of phyloseq-class + --- The following example illustrates using the constructor methods for component data tables. @@ -382,6 +388,7 @@ Once you have a phyloseq object available, many accessor functions are available --- + Function | Returns --- | --- `[` | Standard extraction operator. Works on `otu_table`, `sample_data`, and `taxonomyTable` @@ -403,6 +410,7 @@ Function | Returns `taxa_are_rows` | `TRUE` if taxa are row indices in `otu_table` `tax_table` | A taxonomy table `phy_tree` | Access the tree contained in a phyloseq object + ---