### Install phyloseq using BiocManager

Source: https://github.com/joey711/phyloseq/blob/master/README.md

Installs the phyloseq package using BiocManager. Ensure BiocManager is installed first if necessary.

```R
if(!requireNamespace("BiocManager")){
  install.packages("BiocManager")
}
BiocManager::install("phyloseq")
```

--------------------------------

### Document Setup and Support Detection

Source: https://github.com/joey711/phyloseq/blob/master/README.html

This section sets up document-specific properties and detects browser support for various features.

```JavaScript
c = ga.support = {},
    f = ga.isXML = function(a) {
        var b = a && (a.ownerDocument || a).documentElement;
        return b ? "HTML" !== b.nodeName : !1
    },
    m = ga.setDocument = function(a) {
        var b, e, g = a ? a.ownerDocument || a : v;
        return g !== n && 9 === g.nodeType && g.documentElement ? (n = g, o = g.documentElement, e = g.defaultView, e && e !== e.top && (e.addEventListener ? e.addEventListener("unload", ea, !1) : e.attachEvent && e.attachEvent("onunload", ea)), p = !f(g), c.attributes = ja(function(a) {
            return a.className = "i", !a.getAttribute("className")
        }), c.getElementsByTagName = ja(function(a) {
            return a.appendChild(g.createComment("")), !a.getElementsByTagName("*").length
        }), c.getElementsByClassName = $.test(g.getElementsByClassName),
        c.getById = ja(function(a) {
            return o.appendChild(a).id = u, !g.getElementsByName || !g.getElementsByName(u).length
        }), c.getById ? (d.find.ID = function(a, b) {
            if ("undefined" != typeof b.getElementById && p) {
                var c = b.getElementById(a);
                return c && c.parentNode ? [c] : []
            }
        }, d.filter.ID = function(a) {
            var b = a.replace(ca, da);
            return function(a) {
                return a.getAttribute("id") === b
            }
        }) : (delete d.find.ID, d.filter.ID = function(a) {
            var b = a.replace(ca, da);
            return function(a) {
                var c = "undefined" != typeof a.getAttributeNode && a.getAttributeNode("id");
                return c && c.value === b
            }
        }), d.find.TAG
```

--------------------------------

### Getting Sample Names

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the names of all samples in the phyloseq object.

```r
sample_names(physeq)
```

--------------------------------

### Getting Sample Data as Data Frame

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Converts the sample_data object into a data frame.

```R
sample_df <- as.data.frame(sample_data(physeq_obj))

```

--------------------------------

### Getting Sample Data for Specific Variables

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Extracts specific variables (columns) from the sample data.

```R
# Get 'Treatment' and 'Sex' variables
selected_vars <- get_variable(sample_data(physeq_obj), c("Treatment", "Sex"))

```

--------------------------------

### Getting Sample Data as SampleData Object

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Ensures the sample data is returned as a sample_data object.

```R
sample_data_strict <- sample_data(physeq_obj, errorIfNULL = TRUE)

```

--------------------------------

### Getting Sample Data with Missing Values

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the sample data, handling potential missing values.

```R
sample_with_na <- sample_data(physeq_obj, na.rm = FALSE)

```

--------------------------------

### Getting Sample Data Transposed

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Returns the sample data with metadata variables as rows and samples as columns.

```R
sample_transposed <- t(sample_data(physeq_obj))

```

--------------------------------

### Getting Sample Data as a Matrix with Column Names Only

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the sample data as a matrix, preserving only the column (metadata variable) names.

```r
sample_matrix_col_names <- as(sample_data(physeq), "matrix")
rownames(sample_matrix_col_names) <- NULL
```

--------------------------------

### Load and Inspect a Phyloseq Object

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Loads a phyloseq object from a file and displays its structure. Ensure the 'phyloseq' package is installed and loaded.

```R
library(phyloseq)
# Load the phyloseq object from a file (e.g., .rds)
physeq <- readRDS("path/to/your/phyloseq_object.rds")
# Print the structure of the object
print(physeq)
```

--------------------------------

### Getting Sample Data as Data Frame

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the sample data from the phyloseq object as a data frame.

```r
sample_df <- as.data.frame(sample_data(physeq))
```

--------------------------------

### Create a Phyloseq Object from All Components

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU table, sample data, taxonomy table, and a phylogenetic tree.

```R
library(phyloseq)
# Assuming 'otu_table_data', 'sample_data_frame', 'tax_table_data', 'phylo_tree' are your data
physeq_all <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                       sample_data(sample_data_frame), 
                       tax_table(tax_table_data), 
                       phy_tree(phylo_tree))
```

--------------------------------

### Setting or Getting HTML Content

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Use the .html() method to set or get the HTML content of elements. When setting HTML, it can parse strings and append them as DOM nodes. Be cautious with untrusted HTML strings due to potential security risks.

```javascript
html:function(a){return V(this,function(a){var b=this[0]||{},c=0,d=this.length;if(void 0===a)return 1===b.nodeType?b.innerHTML.replace(fa,""):void 0;if(!("string"!=typeof a||ma.test(a)||!k.htmlSerialize&&ga.test(a)||!k.leadingWhitespace&&ha.test(a)||ra[(ja.exec(a)||["",""])[1].toLowerCase()])){a=a.replace(ia,"<$1></$2>");try{for(;d>c;c++)b=this[c]||{},1===b.nodeType&&(m.cleanData(ua(b,!1)),b.innerHTML=a);b=0}catch(e){}}b&&this.empty().append(a)},null,a,arguments.length)}
```

--------------------------------

### Getting Phylogenetic Tree with Missing Tips

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the phylogenetic tree, potentially handling cases where tips might be missing.

```R
tree_with_missing_tips <- phy_tree(physeq_with_tree, errorIfNULL = FALSE)

```

--------------------------------

### Getting Sample Data as a Character Matrix

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the sample data as a character matrix. Useful for inspecting metadata strings.

```r
sample_char_matrix <- as(sample_data(physeq), "character")
```

--------------------------------

### Getting Sample Data for Specific Samples and Variables (Second Method)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Extracts specific variables from the sample data for a subset of samples using a second method.

```R
# Get 'Treatment' for 'Sample1' and 'Sample2'
sample_subset_vars_alt <- sample_data(physeq_obj)[c("Sample1", "Sample2"), ]$Treatment

```

--------------------------------

### Create a Phyloseq Object from OTU, Taxonomy, and Tree (No Sample Data)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU table, taxonomy table, and a phylogenetic tree. Sample data is not included.

```R
library(phyloseq)
# Assuming 'otu_table_data', 'tax_table_data', 'phylo_tree' are your data
physeq_no_sample <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                             tax_table(tax_table_data), 
                             phy_tree(phylo_tree))
```

--------------------------------

### Getting Sample Size

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the number of samples in the phyloseq object.

```r
nsamples(physeq)
```

--------------------------------

### Getting Sample Data as a Sparse Matrix

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the sample data as a sparse matrix. Note: This is uncommon as sample data is typically dense.

```r
sparse_sample_matrix <- as(sample_data(physeq), "dgCMatrix")
```

--------------------------------

### Getting Phylogenetic Tree for Specific Taxa and Rooting (Second Method)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Prunes the phylogenetic tree to specific taxa and then roots it using a second method.

```R
# Prune tree to 'OTU1', 'OTU2' and root using 'OTU_outgroup'
pruned_tree_alt2 <- prune_taxa(c("OTU1", "OTU2"), phy_tree(physeq_with_tree))
rooted_tree_alt2 <- root(pruned_tree_alt2, outgroup = "OTU_outgroup")

```

--------------------------------

### Create a Phyloseq Object from OTU, Taxonomy, and Tree (No Sample Data)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU table, taxonomy table, and a phylogenetic tree. Sample data is not included.

```R
library(phyloseq)
# Assuming 'otu_table_data', 'tax_table_data', 'phylo_tree' are your data
physeq_no_sample_data <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                                  tax_table(tax_table_data), 
                                  phy_tree(phylo_tree))
```

--------------------------------

### Getting Taxonomy Table as Matrix

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Ensures the taxonomy table is returned as a matrix.

```R
tax_matrix_strict <- tax_table(physeq_obj, errorIfNULL = TRUE)

```

--------------------------------

### Create a Phyloseq Object from OTU, Taxonomy, and Tree (No Sample Data)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU table, taxonomy table, and a phylogenetic tree. Sample data is not included.

```R
library(phyloseq)
# Assuming 'otu_table_data', 'tax_table_data', 'phylo_tree' are your data
physeq_no_sample_data_final <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                                        tax_table(tax_table_data), 
                                        phy_tree(phylo_tree))
```

--------------------------------

### Getting Number of Samples

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Returns the total number of samples in the phyloseq object.

```R
num_samples <- nsamples(physeq_obj)

```

--------------------------------

### Create a Phyloseq Object from OTU, Taxonomy, and Tree (No Sample Data)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU table, taxonomy table, and a phylogenetic tree. Sample data is not included.

```R
library(phyloseq)
# Assuming 'otu_table_data', 'tax_table_data', 'phylo_tree' are your data
physeq_no_sample_data_final_again <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                                              tax_table(tax_table_data), 
                                              phy_tree(phylo_tree))
```

--------------------------------

### Creating a Phyloseq Object with Only OTU Table

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Constructs a phyloseq object using only an OTU table. This is a minimal starting point.

```R
physeq <- otu_table(otu.tab, taxa_are_rows = TRUE)
```

--------------------------------

### Getting Phylogenetic Tree for Specific Taxa and Rooting (Third Method)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Prunes the phylogenetic tree to specific taxa and then roots it using a third method.

```R
# Prune tree to 'OTU1', 'OTU2' and root using 'OTU_outgroup'
pruned_tree_alt3 <- prune_taxa(c("OTU1", "OTU2"), phy_tree(physeq_with_tree))
rooted_tree_alt3 <- root(pruned_tree_alt3, outgroup = "OTU_outgroup")

```

--------------------------------

### Create a Phyloseq Object from OTU, Taxonomy, and Sample Data with Tree

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU table, taxonomy table, sample data, and a phylogenetic tree.

```R
library(phyloseq)
# Assuming 'otu_table_data', 'sample_data_frame', 'tax_table_data', 'phylo_tree' are your data
physeq_full_tree <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                             sample_data(sample_data_frame), 
                             tax_table(tax_table_data), 
                             phy_tree(phylo_tree))
```

--------------------------------

### Getting Taxa Count

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the number of taxa (OTUs/ASVs) in the phyloseq object.

```r
ntaxa(physeq)
```

--------------------------------

### Getting Sample Data for Specific Samples and Variables (Third Method)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Extracts specific variables from the sample data for a subset of samples using a third method.

```R
# Get 'Treatment' for 'Sample1' and 'Sample2'
sample_subset_vars_alt2 <- sample_data(physeq_obj)[c("Sample1", "Sample2"), "Treatment", drop = FALSE]

```

--------------------------------

### Create a Phyloseq Object from OTU and Sample Data with Tree

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU, sample data, and a phylogenetic tree. Taxonomy can be added later.

```R
library(phyloseq)
# Assuming 'otu_table_data', 'sample_data_frame', 'phylo_tree' are your data
physeq_otu_sample_tree <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                                   sample_data(sample_data_frame), 
                                   phy_tree(phylo_tree))
```

--------------------------------

### jQuery Value Manipulation

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Handles getting and setting values for form elements.

```javascript
var lb=/\r/g;m.fn.extend({val:function(a){var b,c,d,e=this[0];{if(arguments.length)return d=m.isFunction(a),this.each(function(c){var e;1===this.nodeType&&(e=d?a.call(this,c,m(this).val()):a,null==e?e="":"number"==typeof e?e+="":"number"==typeof e?e+="":m.isArray(e)&&(e=m.map(e,function(a){return null==a?"":a+""})),b=m.valHooks[this.type]||m.valHooks[this.nodeName.toLowerCase()],b&&"set"in b&&void 0!==b.set(this,e,"value")||(this.value=e))});if(e)return b=m.valHooks[e.type]||m.valHooks[e.nodeName.toLowerCase()],b&&"get"in b&&v
```

--------------------------------

### Getting Sample Data as a Matrix with Row and Column Names

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the sample data as a matrix, preserving row (samples) and column (metadata variable) names.

```r
sample_matrix_named <- as(sample_data(physeq), "matrix")
```

--------------------------------

### Getting Phylogenetic Tree for Specific Taxa and Rooting (Fourth Method)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Prunes the phylogenetic tree to specific taxa and then roots it using a fourth method.

```R
# Prune tree to 'OTU1', 'OTU2' and root using 'OTU_outgroup'
pruned_tree_alt4 <- prune_taxa(c("OTU1", "OTU2"), phy_tree(physeq_with_tree))
rooted_tree_alt4 <- root(pruned_tree_alt4, outgroup = "OTU_outgroup")

```

--------------------------------

### Getting Sample Data as a Matrix with Row Names Only

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the sample data as a matrix, preserving only the row (samples) names.

```r
sample_matrix_row_names <- as(sample_data(physeq), "matrix")
colnames(sample_matrix_row_names) <- NULL
```

--------------------------------

### Create a Phyloseq Object from Sample Data Only

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with only sample metadata. OTU and taxonomy data can be added later.

```R
library(phyloseq)
# Assuming 'sample_data_frame' is your sample data
physeq_sample_only <- phyloseq(sample_data(sample_data_frame))
```

--------------------------------

### Getting Phylogenetic Tree for Specific Taxa and Rooting (Alternative)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Prunes the phylogenetic tree to specific taxa and then roots it using an alternative method.

```R
# Prune tree to 'OTU1', 'OTU2' and root using 'OTU_outgroup'
pruned_tree_alt <- prune_taxa(c("OTU1", "OTU2"), phy_tree(physeq_with_tree))
rooted_tree_alt <- root(pruned_tree_alt, outgroup = "OTU_outgroup")

```

--------------------------------

### Getting Phylogenetic Tree Dimensions

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Returns the number of nodes and tips in the phylogenetic tree.

```R
tree_dims <- dim(phy_tree(physeq_with_tree))

```

--------------------------------

### Getting Sample Data for Specific Samples and Variables (Fourth Method)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Extracts specific variables from the sample data for a subset of samples using a fourth method.

```R
# Get 'Treatment' for 'Sample1' and 'Sample2'
sample_subset_vars_alt3 <- sample_data(physeq_obj)[c("Sample1", "Sample2"), "Treatment", drop = FALSE]

```

--------------------------------

### Getting Number of Taxa

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Returns the total number of taxa (OTUs/ASVs) in the phyloseq object.

```R
num_taxa <- ntaxa(physeq_obj)

```

--------------------------------

### Create a Phyloseq Object from OTU and Sample Data

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU and sample data. Taxonomy can be added later.

```R
library(phyloseq)
# Assuming 'otu_table_data' and 'sample_data_frame' are your data
physeq_otu_sample <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                              sample_data(sample_data_frame))
```

--------------------------------

### Getting Taxonomy Table as a Matrix

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the taxonomy table from the phyloseq object as a matrix.

```r
tax_matrix <- as(tax_table(physeq), "matrix")
```

--------------------------------

### Create a Phyloseq Object from OTU, Sample, and Taxonomy Tables

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU, sample, and taxonomy data. A phylogenetic tree can be added subsequently.

```R
library(phyloseq)
# Assuming 'otu_table_data', 'sample_data_frame', 'tax_table_data' are your data
physeq_full <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                        sample_data(sample_data_frame), 
                        tax_table(tax_table_data))
```

--------------------------------

### Create a Phyloseq Object from OTU, Taxonomy, and Sample Data (No Tree)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU table, taxonomy table, and sample data. A phylogenetic tree is not included.

```R
library(phyloseq)
# Assuming 'otu_table_data', 'sample_data_frame', 'tax_table_data' are your data
physeq_no_tree <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                           sample_data(sample_data_frame), 
                           tax_table(tax_table_data))
```

--------------------------------

### Getting OTU Table as Matrix

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the OTU table from the phyloseq object as a matrix.

```r
otu_matrix <- as(otu_table(physeq), "matrix")
```

--------------------------------

### Getting Sample Data for Specific Samples and Variables (Alternative)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Extracts specific variables from the sample data for a subset of samples using a different method.

```R
# Get 'Treatment' for 'Sample1' and 'Sample2'
sample_subset_vars <- sample_data(physeq_obj)[c("Sample1", "Sample2"), "Treatment", drop = FALSE]

```

--------------------------------

### Getting Sample Data as a Numeric Matrix

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the sample data as a numeric matrix. Note: This will coerce non-numeric data to numeric, potentially losing information.

```r
sample_numeric_matrix <- as(sample_data(physeq), "matrix")
```

--------------------------------

### Getting OTU Table

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the raw OTU count table from the phyloseq object.

```r
otu_table(physeq)
```

--------------------------------

### Create a Sample Data Object

Source: https://github.com/joey711/phyloseq/blob/master/README.html

This snippet demonstrates how to create a basic sample data object using phyloseq. It's useful for testing or when you have small, custom datasets.

```R
library(phyloseq)

# Sample data
OTU = otu_table(matrix(sample(1:1000, 100, replace = TRUE), nrow=10, ncol=10), taxa_are_rows = TRUE)
SAM = sample_data(data.frame( 
  SampleID = paste("Sample", 1:10, sep="_"), 
  Treatment = factor(rep(c("A", "B"), each = 5)), 
  Sex = factor(rep(c("M", "F"), 5)) 
))

# Create phyloseq object
physeq_obj <- phyloseq(OTU, SAM)
print(physeq_obj)
```

--------------------------------

### Create a Phyloseq Object from OTU and Taxonomy Tables

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU and taxonomy tables. Sample data can be added later.

```R
library(phyloseq)
# Assuming 'otu_table_data' and 'tax_table_data' are your data
physeq_otu_tax <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                           tax_table(tax_table_data))
```

--------------------------------

### Getting Taxa Names

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the names of all taxa (OTUs/ASVs) present in the phyloseq object.

```r
taxa_names(physeq)
```

--------------------------------

### Create a Phyloseq Object from OTU and Phylogenetic Tree

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU table and a phylogenetic tree. Sample data and taxonomy can be added later.

```R
library(phyloseq)
# Assuming 'otu_table_data' and 'phylo_tree' are your data
physeq_otu_tree <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                            phy_tree(phylo_tree))
```

--------------------------------

### Creating a Phyloseq Object with Multiple Components

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Demonstrates the creation of a phyloseq object by combining various components like OTU table, taxonomy table, sample data, and phylogenetic tree.

```R
physeq <- phyloseq(otu_table(otu.tab, taxa_are_rows = TRUE), 
                   tax_table(as.matrix(tax.tab)), 
                   sample_data(sample.dat),
                   phy_tree(tree.obj))
```

--------------------------------

### Getting Phylogenetic Tree for Specific Taxa

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Prunes the phylogenetic tree to include only the specified taxa.

```R
# Prune tree to include 'OTU1' and 'OTU2'
pruned_tree <- prune_taxa(c("OTU1", "OTU2"), phy_tree(physeq_with_tree))

```

--------------------------------

### Initialize Modal with JavaScript

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Use this method to programmatically show or hide a modal. Pass 'show' to display it or 'hide' to close it. Options can be passed as the second argument.

```javascript
function b(b,d){return this.each(function(){var e=a(this),f=e.data("bs.modal"),g=a.extend({},c.DEFAULTS,e.data(),{"object"==typeof b&&b});f||e.data("bs.modal",f=new c(this,g)),"string"==typeof b?f[b](d):g.show&&f.show(d)})}
```

--------------------------------

### Getting Phylogenetic Tree as Adjacency Matrix

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Converts the phylogenetic tree into an adjacency matrix representation.

```R
tree_adj_matrix <- as.adjM(phy_tree(physeq_with_tree))

```

--------------------------------

### Create a Phyloseq Object from OTU, Taxonomy, and Tree

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with OTU table, taxonomy table, and a phylogenetic tree. Sample data can be added later.

```R
library(phyloseq)
# Assuming 'otu_table_data', 'tax_table_data', 'phylo_tree' are your data
physeq_otu_tax_tree <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE), 
                                tax_table(tax_table_data), 
                                phy_tree(phylo_tree))
```

--------------------------------

### Getting OTU Table with Specific Samples and Taxa (Alternative)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Extracts the OTU table, filtering for specific samples and taxa using a different syntax.

```R
# Get OTU table for 'OTU1' from 'Sample1' and 'Sample2'
specific_samples_otus_alt <- otu_table(physeq_obj, taxa_are_rows = TRUE)["OTU1", c("Sample1", "Sample2")]

```

--------------------------------

### Importing OTU Table and Metadata

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Load an OTU table and sample metadata from CSV files. Ensure the sample names in the metadata match the column names of the OTU table.

```R
library(phyloseq)

# Load OTU table
otu_table <- read.csv("otu_table.csv", row.names=1)

# Load sample metadata
sample_metadata <- read.csv("sample_metadata.csv", row.names=1)

# Create phyloseq object
physeq_obj <- phyloseq(otu_table(otu_table, taxa_are_rows = TRUE), sample_data(sample_metadata))
```

--------------------------------

### Getting OTU Table Transposed

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Returns the OTU table with samples as rows and taxa as columns.

```R
otu_transposed <- t(otu_table(physeq_obj))

```

--------------------------------

### Getting Taxonomy Table as Data Frame

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Converts the taxonomy table matrix into a data frame.

```R
tax_df <- as.data.frame(tax_table(physeq_obj))

```

--------------------------------

### Creating a Phyloseq Object from Scratch

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Constructs a phyloseq object by providing OTU table, taxonomy table, sample data, and tree directly.

```R
physeq_new <- phyloseq(
  otu_table = otu_table(OTU, taxa_are_rows = TRUE),
  tax_table = tax_table(TAX),
  sample_data = sample_data(sample_data),
  phy_tree = tree_obj
)

```

--------------------------------

### Getting OTU Table with Specific Samples and Taxa (Third Method)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Extracts the OTU table, filtering for specific samples and taxa using a third method.

```R
# Get OTU table for 'OTU1' from 'Sample1' and 'Sample2'
specific_samples_otus_alt2 <- otu_table(physeq_obj, taxa_are_rows = TRUE)[, "Sample1", drop = FALSE]
specific_samples_otus_alt2 <- specific_samples_otus_alt2["OTU1", , drop = FALSE]

```

--------------------------------

### Getting OTU Table with Specific Samples and Taxa (Fourth Method)

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Extracts the OTU table, filtering for specific samples and taxa using a fourth method.

```R
# Get OTU table for 'OTU1' from 'Sample1' and 'Sample2'
specific_samples_otus_alt3 <- otu_table(physeq_obj, taxa_are_rows = TRUE)["OTU1", , drop = FALSE]
specific_samples_otus_alt3 <- specific_samples_otus_alt3[, c("Sample1", "Sample2")]

```

--------------------------------

### Create a Phyloseq Object from OTU Table Only

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with only an OTU table. Sample data and taxonomy can be added later.

```R
library(phyloseq)
# Assuming 'otu_table_data' is your OTU matrix
physeq_otu_only <- phyloseq(otu_table(otu_table_data, taxa_are_rows = TRUE))
```

--------------------------------

### Getting Sample Names

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves a character vector of all sample names present in the phyloseq object.

```R
sample_names <- sample_names(physeq_obj)

```

--------------------------------

### Getting Phylogenetic Tree for Specific Taxa and Rooting

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Prunes the phylogenetic tree to specific taxa and then roots it.

```R
# Prune tree to 'OTU1', 'OTU2' and root using 'OTU_outgroup'
pruned_rooted_tree <- root(prune_taxa(c("OTU1", "OTU2"), phy_tree(physeq_with_tree)), 
                         outgroup = "OTU_outgroup")

```

--------------------------------

### Creating a Phyloseq Object with OTU, Taxonomy, Sample Data, and Tree

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Constructs a complete phyloseq object including OTU table, taxonomy table, sample data, and a phylogenetic tree.

```R
physeq <- phyloseq(otu_table(otu.tab, taxa_are_rows = TRUE), tax_table(as.matrix(tax.tab)), sample_data(sample.dat), phy_tree(tree.obj))
```

--------------------------------

### Tooltip Initialization and Placement

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a tooltip on an element and handles its placement logic, including auto-adjustment based on viewport boundaries. Ensure the tooltip's template and container options are correctly configured.

```javascript
c.prototype.show=function(b){var a=this,c=a.tip(),d=a.getUID(a.type);if(a.isWithContent()&&a.enabled){var e=a.tip();a.fixTitle();e.attr("id",d),a.$element.attr("aria-describedby",d),a.options.animation&&e.addClass("fade");var f="function"==typeof a.options.placement?a.options.placement.call(a,e[0],a.$element[0]):a.options.placement,g=/\s?auto?\s?/i,h=g.test(f);h&&(f=f.replace(g,"")||"top"),e.detach().css({top:0,left:0,display:"block"}).addClass(f).data("bs."+a.type,a),a.options.container?e.appendTo(a.options.container):e.insertAfter(a.$element),a.$element.trigger("inserted.bs."+a.type);var i=a.getPosition(),j=e[0].offsetWidth,k=e[0].offsetHeight;if(h){var l=f,m=a.getPosition(a.$viewport);f="bottom"==f&&i.bottom+k>m.bottom?"top":"top"==f&&i.top-k<m.top?"bottom":"right"==f&&i.right+j>m.width?"left":"left"==f&&i.left-j<m.left?"right":f,e.removeClass(l).addClass(f)}var n=a.getCalculatedOffset(f,i,j,k);a.applyPlacement(n,f);var o=function(){var b=a.hoverState;a.$element.trigger("shown.bs."+a.type),a.hoverState=null,"out"==b&&a.leave(a)};a.support.transition&&a.$tip.hasClass("fade")?e.one("bsTransitionEnd",o).emulateTransitionEnd(c.TRANSITION_DURATION):o()}}
```

--------------------------------

### Getting Phylogenetic Tree Rooted by Taxon

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Roots the phylogenetic tree using a specified taxon as the outgroup.

```R
# Root the tree using 'OTU_outgroup' as the outgroup
rooted_tree_taxon <- root(phy_tree(physeq_with_tree), outgroup = "OTU_outgroup")

```

--------------------------------

### Create a Phyloseq Object from Taxonomy Table Only

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Initializes a phyloseq object with only a taxonomy table. OTU and sample data can be added later.

```R
library(phyloseq)
# Assuming 'tax_table_data' is your taxonomy table
physeq_tax_only <- phyloseq(tax_table(tax_table_data))
```

--------------------------------

### Importing Sample Data

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Loads sample metadata into a phyloseq object. Sample names in the metadata must match OTU table row names.

```R
sample_data_file = "sample_data.txt"
sample_data <- read.delim(sample_data_file, row.names=1)

# Add sample data to phyloseq object
physeq_obj <- phyloseq(otu_table(OTU, taxa_are_rows = TRUE), 
                       tax_table(TAX),
                       sample_data(sample_data))

```

--------------------------------

### Getting Taxonomy Table with Specific Ranks

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Extracts the taxonomy table, filtering for specific taxonomic ranks.

```R
# Get Kingdom, Phylum, and Class ranks
selected_ranks <- tax_table(physeq_obj)[, c("Kingdom", "Phylum", "Class")]

```

--------------------------------

### Create a Phyloseq Object from OTU Table, Taxonomy, and Sample Data

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Demonstrates creating a phyloseq object by combining separate data frames for OTU counts, taxonomic assignments, and sample metadata. Ensure all data frames are properly formatted.

```R
library(phyloseq)
# Assuming otu_table, tax_table, and sample_data are data frames
# Convert data frames to phyloseq objects
OTU <- otu_table(otu_table, taxa_are_rows = TRUE)
TAX <- tax_table(tax_table)
SAMP <- sample_data(sample_data)
# Merge into a single phyloseq object
physeq <- phyloseq(OTU, TAX, SAMP)
```

--------------------------------

### Getting Phylogenetic Tree as Phylo Object

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Ensures the phylogenetic tree is returned as an ape phylo object.

```R
tree_phylo_strict <- phy_tree(physeq_with_tree, errorIfNULL = TRUE)

```

--------------------------------

### Creating a Phyloseq Object from Separate Files

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Demonstrates how to combine different data components (OTU table, taxonomy, tree, sample data) stored in separate files into a single phyloseq object.

```R
library(phyloseq)

# Load data from separate files
otu_table <- read.csv("otu_data.csv", row.names = 1)
taxonomy_table <- read.csv("taxonomy_data.csv", row.names = 1)
sample_data_frame <- read.csv("sample_metadata.csv", row.names = 1)
phylo_tree <- read_tree("tree_data.nwk")

# Create phyloseq objects for each component
otu_physeq <- otu_table(otu_table, taxa_are_rows = TRUE)
tax_physeq <- tax_table(as.matrix(taxonomy_table))
samp_physeq <- sample_data(sample_data_frame)
tree_physeq <- phy_tree(phylo_tree)

# Merge all components into a single phyloseq object
physeq_combined <- phyloseq(otu_physeq, tax_physeq, samp_physeq, tree_physeq)

# Print the combined object
print(physeq_combined)

```

--------------------------------

### Getting OTU Table as Matrix

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Ensures the OTU table is returned as a matrix, regardless of its internal representation.

```R
otu_matrix_strict <- otu_table(physeq_obj, taxa_are_rows = TRUE, errorIfNULL = TRUE)

```

--------------------------------

### Getting Sample Data for Specific Samples

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Extracts the sample data, filtering for a specific set of samples.

```R
# Get sample data for 'Sample1' and 'Sample2'
selected_samples <- sample_data(physeq_obj)[c("Sample1", "Sample2"), ]

```

--------------------------------

### Importing Sample Data from CSV

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Load sample metadata from a CSV file into a phyloseq object. The CSV should have sample IDs as row names and metadata variables as columns.

```R
library(phyloseq)

# Assuming 'sample_data.csv' has sample IDs in rows and metadata in columns
SAM_table <- read.csv("sample_data.csv", row.names=1)
SAM <- sample_data(SAM_table)

# Create a minimal phyloseq object with just the sample data
physeq_obj <- phyloseq(SAM)
print(physeq_obj)
```

--------------------------------

### Show Modal Method

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Handles the logic for displaying a modal, including triggering events, setting states, and managing focus and backdrop.

```javascript
c.prototype.show=function(b){var d=this,e=a.Event("show.bs.modal",{relatedTarget:b});this.$element.trigger(e),this.isShown||e.isDefaultPrevented()||(this.isShown=!0,this.checkScrollbar(),this.setScrollbar(),this.$body.addClass("modal-open"),this.escape(),this.resize(),this.$element.on("click.dismiss.bs.modal",'\\[data-dismiss="modal"\\]',a.proxy(this.hide,this)),this.$dialog.on("mousedown.dismiss.bs.modal",function(){d.$element.one("mouseup.dismiss.bs.modal",function(b){a(b.target).is(d.$element)&&(d.ignoreBackdropClick=!0)})}),this.backdrop(function(){var e=a.support.transition&&d.$element.hasClass("fade");d.$element.parent().length||d.$element.appendTo(d.$body),d.$element.show().scrollTop(0),d.adjustDialog(),e&&d.$element[0].offsetWidth,d.$element.addClass("in"),d.enforceFocus();var f=a.Event("shown.bs.modal",{relatedTarget:b});e?d.$dialog.one("bsTransitionEnd",function(){d.$element.trigger("focus").trigger(f)}).emulateTransitionEnd(c.TRANSITION_DURATION):d.$element.trigger("focus").trigger(f)}))}
```

--------------------------------

### Getting Taxonomy Table with Specific Taxa

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Extracts the taxonomy table, filtering for a specific set of taxa.

```R
# Get taxonomy for 'OTU1' and 'OTU2'
selected_tax <- tax_table(physeq_obj)[c("OTU1", "OTU2"), ]

```

--------------------------------

### Getting OTU Table with Specific Taxa

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Extracts the OTU table, filtering for a specific set of taxa.

```R
# Get OTU table for 'OTU1' and 'OTU2'
selected_otus <- otu_table(physeq_obj, taxa_are_rows = TRUE)[c("OTU1", "OTU2"), ]

```

--------------------------------

### Importing OTU Table and Taxonomy

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Loads an OTU table and its corresponding taxonomy into phyloseq objects. Ensure the file paths are correct.

```R
library(phyloseq)
library(ape)
library(vegan)

# Load OTU table
otu <- read.csv("/Users/joey711/Documents/GitHub/phyloseq/data-raw/otu_table.csv")

# Load taxonomy table
tax <- read.csv("/Users/joey711/Documents/GitHub/phyloseq/data-raw/taxonomy.csv")

# Create phyloseq object
physeq <- phyloseq(otu_table(otu, taxa_are_rows = TRUE), 
                   tax_table(tax))

# Print the object
print(physeq)
```

--------------------------------

### Data Import from QIIME Format

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Loads data directly from QIIME output files (e.g., otu_table.biom, taxonomy.qza). Requires the 'qiime2R' package.

```R
library(phyloseq)
library(qiime2R)

# Path to QIIME files
biom_file <- "otu_table.biom"
tax_file <- "taxonomy.qza"
map_file <- "mapping.txt"

# Read data into phyloseq object
physeq_qiime <- q2_to_phyloseq(otu.path = biom_file, 
                                 tax.path = tax_file, 
                                 map.path = map_file)
```

--------------------------------

### Getting Taxonomy Table Transposed

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Returns the taxonomy table with taxa as rows and taxonomic ranks as columns.

```R
tax_transposed <- t(tax_table(physeq_obj))

```

--------------------------------

### Creating a Phyloseq Object from Multiple Data Sources

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Construct a phyloseq object by combining OTU table, sample metadata, and taxonomic information. The `tax_table` should have columns for each taxonomic rank.

```R
library(phyloseq)

otu <- otu_table(read.csv("otu_table.csv", row.names=1), taxa_are_rows = TRUE)
sampledata <- sample_data(read.csv("sample_metadata.csv", row.names=1))
tax <- tax_table(as.matrix(read.csv("tax_table.csv", row.names=1)))

physeq <- phyloseq(otu, sampledata, tax)
```

--------------------------------

### Getting Mean Reads per Sample

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Calculates the mean number of reads per sample for each taxon.

```R
mean_reads_per_sample_taxon <- taxa_mean_fun(physeq_obj)

```

--------------------------------

### Creating a Phyloseq Object with OTU, Taxonomy, and Sample Data

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Constructs a phyloseq object using OTU table, taxonomy table, and sample data. A phylogenetic tree is not included.

```R
physeq <- phyloseq(otu_table(otu.tab, taxa_are_rows = TRUE), tax_table(as.matrix(tax.tab)), sample_data(sample.dat))
```

--------------------------------

### Getting Total Reads per Sample

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Calculates the total number of reads for each sample in the phyloseq object.

```R
total_reads_per_sample <- sample_sums(physeq_obj)

```

--------------------------------

### Importing OTU Table and Taxonomy

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Loads an OTU table and taxonomy data from CSV files. Ensure the files are correctly formatted.

```R
library(phyloseq)
library(vegan)

# Load data
# otu.tab <- read.csv("otu_table.csv", row.names=1)
# tax.tab <- read.csv("taxonomy.csv", row.names=1)
# sample.dat <- read.csv("sample_data.csv", row.names=1)

# Create phyloseq object
# otu.phyloseq <- otu_table(otu.tab, taxa_are_rows = TRUE)
# tax.phyloseq <- tax_table(as.matrix(tax.tab))
# sample.phyloseq <- sample_data(sample.dat)

# physeq <- phyloseq(otu.phyloseq, tax.phyloseq, sample.phyloseq)
```

--------------------------------

### Creating a Phyloseq Object from Scratch

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Constructs a phyloseq object using individual components like OTU table, sample data, and phylogenetic tree. This is useful for creating objects programmatically.

```R
library(phyloseq)
library(ape)
library(vegan)

# Create an example OTU table
otu_data <- matrix(sample(1:1000, 1000), nrow = 10, ncol = 10)
rownames(otu_data) <- paste0("OTU", 1:10)
colnames(otu_data) <- paste0("Sample", 1:10)

# Create an example taxonomy table
tax_data <- matrix(c(sample(letters, 10), sample(letters, 10), sample(letters, 10), sample(letters, 10), sample(letters, 10)), nrow = 10, ncol = 5)
rownames(tax_data) <- paste0("OTU", 1:10)
colnames(tax_data) <- c("Kingdom", "Phylum", "Class", "Order", "Family")

# Create an example sample data frame
sample_data_df <- data.frame(Treatment = sample(c("Control", "Treated"), 10, replace = TRUE))
rownames(sample_data_df) <- paste0("Sample", 1:10)

# Create an example phylogenetic tree
tree <- rtree(10, rooted=TRUE, tip.label=paste0("OTU", 1:10))

# Create the phyloseq object
physeq_obj <- phyloseq(otu_table(otu_data, taxa_are_rows = TRUE), 
                       tax_table(tax_data), 
                       sample_data(sample_data_df), 
                       phy_tree(tree))

# Print the object
print(physeq_obj)
```

--------------------------------

### Getting Taxa Names

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves a character vector of all taxa (OTU/ASV) names present in the phyloseq object.

```R
taxa_names <- taxa_names(physeq_obj)

```

--------------------------------

### Getting OTU Table as a Data Frame

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Retrieves the OTU table from the phyloseq object as a data frame.

```r
otu_df <- as.data.frame(otu_table(physeq))
```

--------------------------------

### Creating a Phyloseq Object with OTU and Sample Data

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Constructs a phyloseq object using an OTU table and sample data. Taxonomy information is not included.

```R
physeq <- phyloseq(otu_table(otu.tab, taxa_are_rows = TRUE), sample_data(sample.dat))
```

--------------------------------

### Importing OTU Table

Source: https://github.com/joey711/phyloseq/blob/master/README.html

Loads an OTU table from a file. Ensure the file path is correct.

```r
otu_table <- read.csv("otu_table.csv")
```

--------------------------------

### HTML5 Shiv Initialization

Source: https://github.com/joey711/phyloseq/blob/master/README.html

This snippet shows the basic initialization of HTML5 Shiv. It ensures that HTML5 elements are recognized and styled correctly in older browsers like Internet Explorer. Ensure this script is placed in the <head> of your HTML document.

```javascript
!function(a,b){function c(a,b){var c=b.createElement("p"),d=b.getElementsByTagName("head")[0]||b.documentElement;return c.innerHTML="<a href=\"//</a>"></a>"+a,d.insertBefore(c,d.firstChild),c.firstChild.nodeName.toLowerCase()}
```

```javascript
function d(){var a=f.elements;return"string"==typeof a?a.split(" "):a}function e(a,b,c,d){this.elements=a,this.content=c,this.hidden=d,this.callFn=b}
```

```javascript
e.prototype.render=function(){var a=this.content;if("undefined"==typeof this.hidden)return a;var b=f.createElement(this.elements),c=b.style;return c.behavior="url(#default#VML)",this.hidden==="*"?b.innerHTML=a:b.setAttribute(""+this.hidden,a),b}
```

```javascript
function f(a){var b=a.elements;if(b){if("object"==typeof b)return b;if("string"==typeof b)return b.split(" ")}
```

```javascript
return["abbr","article","aside","audio","bdi","canvas","data","datalist","details","dialog","figcaption","figure","footer","header","hgroup","main","mark","meter","nav","output","picture","progress","section","summary","time","video"]}
```

```javascript
function g(a){var b=f(a),c=b.elements,d=b.shivCSS,e=b.supportsUnknownElements;if(!e){return a.createDocumentFragment()}}function h(a,b){var c=f(a),d=c.elements,e=c.hidden,g=c.shivMethods;if(!g||!d||!d.length)return b.createDocumentFragment();var h=b.createDocumentFragment(),i=h.createElement,j=h.createDocumentFragment;h.createElement=function(){for(var a,b=0,c=d.length;c>b;b++)a=d[b];return i(a)};var k=/\[\w\-:]+/g;return h.createDocumentFragment=function(){var a=j();return h.shivMethods&&k.test(a.lastChild.nodeName)&&(h.frag.createElem(a.lastChild),h.frag.createElem(a.lastChild.nodeName)),a},h}
```

```javascript
function j(a){a||(a=b);var d=f(a);return!t.shivCSS||k||d.hasCSS||(d.hasCSS=!!c(a,"article,aside,dialog,figcaption,figure,footer,header,hgroup,main,nav,section{display:block}mark{background:#FF0;color:#000}template{display:none}")),l||i(a,d),a}var k,l,m="3.7.2",n=a.html5||{},o=/^<|^(?:button|map|select|textarea|object|iframe|option|optgroup)$/i,p=/^(?:a|b|code|div|fieldset|h1|h2|h3|h4|h5|h6|i|label|li|ol|p|q|span|strong|style|table|tbody|td|th|tr|ul)$/i,q="\_html5shiv",r=0,s={};!function(){try{var a=b.createElement("a");a.innerHTML="<xyz></xyz>",k="hidden"in a,l=1==a.childNodes.length||function(){b.createElement("a");var a=b.createDocumentFragment();return"undefined"==typeof a.cloneNode||"undefined"==typeof a.createDocumentFragment||"undefined"==typeof a.createElement}()}}catch(c){k=!0,l=!0}}();var t={elements:n.elements||"abbr article aside audio bdi canvas data datalist details dialog figcaption figure footer header hgroup main mark meter nav output picture progress section summary template time video",version:m,shivCSS:n.shivCSS!==!1,supportsUnknownElements:l,shivMethods:n.shivMethods!==!1,type:"default",shivDocument:j,createElement:g,createDocumentFragment:h,addElements:e};a.html5=t,j(b)}(this,document);
```