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Fix tables and Bioconductor build #1777

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Fix tables and Bioconductor build #1777

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8 changes: 8 additions & 0 deletions vignettes/phyloseq-basics.Rmd
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Expand Up @@ -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
Expand Down Expand Up @@ -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 <a id="table:build"></a>

---

Function | Input Class | Output Description
--- | --- | ---
`otu_table` | numeric matrix | `otu_table` object storing OTU abundance
Expand All @@ -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.
Expand Down Expand Up @@ -382,6 +388,7 @@ Once you have a phyloseq object available, many accessor functions are available
<a id="table:access"></a>

---

Function | Returns
--- | ---
`[` | Standard extraction operator. Works on `otu_table`, `sample_data`, and `taxonomyTable`
Expand All @@ -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

---


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