create_heatmap_plot

Create heatmap visualization of GSEA results

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

create_heatmap_plot function

<dl><dt>gsea_results</dt>
<dd>A data frame containing GSEA results from the pathway_gsea function</dd>
<dt>abundance</dt>
<dd>A data frame containing the original abundance data</dd>
<dt>metadata</dt>
<dd>A data frame containing sample metadata</dd>
<dt>group</dt>
<dd>A character string specifying the column name in metadata that contains the grouping variable</dd>
<dt>n_pathways</dt>
<dd>An integer specifying the number of pathways to display</dd>
<dt>cluster_rows</dt>
<dd>A logical value indicating whether to cluster rows</dd>
<dt>cluster_columns</dt>
<dd>A logical value indicating whether to cluster columns</dd>
<dt>show_rownames</dt>
<dd>A logical value indicating whether to show row names</dd>
<dt>annotation_colors</dt>
<dd>A list of colors for annotations</dd></dl>

Arguments

Create heatmap visualization of GSEA results — create_heatmap_plot

<dl>

<dt>gsea_results</dt>
<dd>A data frame containing GSEA results from the pathway_gsea function</dd>


<dt>abundance</dt>
<dd>A data frame containing the original abundance data</dd>


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


<dt>group</dt>
<dd>A character string specifying the column name in metadata that contains the grouping variable</dd>


<dt>n_pathways</dt>
<dd>An integer specifying the number of pathways to display</dd>


<dt>cluster_rows</dt>
<dd>A logical value indicating whether to cluster rows</dd>


<dt>cluster_columns</dt>
<dd>A logical value indicating whether to cluster columns</dd>


<dt>show_rownames</dt>
<dd>A logical value indicating whether to show row names</dd>


<dt>annotation_colors</dt>
<dd>A list of colors for annotations</dd>

</dl>

create_heatmap_plot: Create heatmap visualization of GSEA results

Description

Usage

Value

Arguments