calculate_abundance_stats

This function calculates mean relative abundance, standard deviation, and log2 fold change
for each feature between two groups.

internal

Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <doi:10.1093/bioinformatics/btad470>.

Chen Yang

ggpicrust2

Make 'PICRUSt2' Output Analysis and Visualization Easier

calculate_abundance_stats function

<dl><dt>abundance</dt>
<dd>A matrix or data frame with features as rows and samples as columns</dd>
<dt>metadata</dt>
<dd>A data frame containing sample information</dd>
<dt>group</dt>
<dd>Character string specifying the group column name in metadata</dd>
<dt>features</dt>
<dd>Character vector of feature names to calculate statistics for</dd>
<dt>group1</dt>
<dd>Character string specifying the first group name</dd>
<dt>group2</dt>
<dd>Character string specifying the second group name</dd></dl>

Arguments

Helper function to calculate abundance statistics for differential analysis — calculate_abundance_stats

<dl>

<dt>abundance</dt>
<dd>A matrix or data frame with features as rows and samples as columns</dd>


<dt>metadata</dt>
<dd>A data frame containing sample information</dd>


<dt>group</dt>
<dd>Character string specifying the group column name in metadata</dd>


<dt>features</dt>
<dd>Character vector of feature names to calculate statistics for</dd>


<dt>group1</dt>
<dd>Character string specifying the first group name</dd>


<dt>group2</dt>
<dd>Character string specifying the second group name</dd>

</dl>

calculate_abundance_stats: Helper function to calculate abundance statistics for differential analysis

Description

Usage

Value

Arguments