prepare_gene_sets

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

prepare_gene_sets function

<dl><dt>pathway_type</dt>
<dd>A character string specifying the pathway type: "KEGG", "MetaCyc", or "GO"</dd>
<dt>organism</dt>
<dd>A character string specifying the organism (only relevant for KEGG and GO)</dd>
<dt>go_category</dt>
<dd>A character string specifying the GO category to use.
"all" (default) uses all categories. Valid values are determined by
the reference data; see <code>table(ko_to_go_reference$category)</code>.</dd></dl>

Arguments

Prepare gene sets for GSEA — prepare_gene_sets

<dl>

<dt>pathway_type</dt>
<dd>A character string specifying the pathway type: "KEGG", "MetaCyc", or "GO"</dd>


<dt>organism</dt>
<dd>A character string specifying the organism (only relevant for KEGG and GO)</dd>


<dt>go_category</dt>
<dd>A character string specifying the GO category to use.
"all" (default) uses all categories. Valid values are determined by
the reference data; see <code>table(ko_to_go_reference$category)</code>.</dd>

</dl>

prepare_gene_sets: Prepare gene sets for GSEA

Description

Usage

Value

Arguments