create_network_plot

Create network 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_network_plot function

<dl><dt>gsea_results</dt>
<dd>A data frame containing GSEA results from the pathway_gsea function</dd>
<dt>similarity_measure</dt>
<dd>A character string specifying the similarity measure: "jaccard", "overlap", or "correlation"</dd>
<dt>similarity_cutoff</dt>
<dd>A numeric value specifying the similarity threshold for filtering connections</dd>
<dt>n_pathways</dt>
<dd>An integer specifying the number of pathways to display</dd>
<dt>layout</dt>
<dd>A character string specifying the network layout algorithm: "fruchterman", "kamada", or "circle"</dd>
<dt>node_color_by</dt>
<dd>A character string specifying the node color mapping: "NES", "pvalue", or "p.adjust"</dd>
<dt>edge_width_by</dt>
<dd>A character string specifying the edge width mapping: "similarity" or "constant"</dd></dl>

Arguments

Create network visualization of GSEA results — create_network_plot

<dl>

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


<dt>similarity_measure</dt>
<dd>A character string specifying the similarity measure: "jaccard", "overlap", or "correlation"</dd>


<dt>similarity_cutoff</dt>
<dd>A numeric value specifying the similarity threshold for filtering connections</dd>


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


<dt>layout</dt>
<dd>A character string specifying the network layout algorithm: "fruchterman", "kamada", or "circle"</dd>


<dt>node_color_by</dt>
<dd>A character string specifying the node color mapping: "NES", "pvalue", or "p.adjust"</dd>


<dt>edge_width_by</dt>
<dd>A character string specifying the edge width mapping: "similarity" or "constant"</dd>

</dl>

create_network_plot: Create network visualization of GSEA results

Description

Usage

Value

Arguments