plotGSEA

The <code>plotGSEA</code> function visualizes the results of a GSEA (Gene Set Enrichment Analysis) using data from
the <code>fgsea</code> package. It generates a composite plot that includes an enrichment plot and a ranked metric plot.

Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker2.0' database (see Xia Li, Peng Wang, Yunpeng Zhang (2023) <doi: 10.1093/nar/gkac947>). Streamlines biological label assignment in single-cell RNA-seq data and facilitates transcriptomic analysis, including preparation of TCGA<https://portal.gdc.cancer.gov/> and GEO<https://www.ncbi.nlm.nih.gov/geo/> datasets, differential expression analysis and visualization of enrichment analysis results. Additional utility functions support various bioinformatics workflows. See Wei Cui (2024) <doi: 10.1101/2024.09.14.609619> for more details.

Wei Cui

easybio

Comprehensive Single-Cell Annotation and Transcriptomic Analysis
Toolkit

plotGSEA function

<dl><dt>fgseaRes</dt>
<dd>A data table containing the GSEA results from the <code>fgsea</code> package.</dd>
<dt>pathways</dt>
<dd>A list of all pathways used in the GSEA analysis.</dd>
<dt>pwayname</dt>
<dd>The name of the pathway to visualize.</dd>
<dt>stats</dt>
<dd>A numeric vector representing the ranked statistics.</dd>
<dt>save</dt>
<dd>A logical value indicating whether to save the plot as a PDF file. Default is <code>FALSE</code>.</dd></dl>

Arguments

Visualization of GSEA Result from fgsea::fgsea() — plotGSEA

<dl>

<dt>fgseaRes</dt>
<dd>A data table containing the GSEA results from the <code>fgsea</code> package.</dd>


<dt>pathways</dt>
<dd>A list of all pathways used in the GSEA analysis.</dd>


<dt>pwayname</dt>
<dd>The name of the pathway to visualize.</dd>


<dt>stats</dt>
<dd>A numeric vector representing the ranked statistics.</dd>


<dt>save</dt>
<dd>A logical value indicating whether to save the plot as a PDF file. Default is <code>FALSE</code>.</dd>

</dl>

plotGSEA: Visualization of GSEA Result from `fgsea::fgsea()`

Description

Usage

Value

Arguments