plotEnrichment2

This function creates a plot of enrichment scores for a specified pathway.
It provides a visual representation of the enrichment
score (ES) along with the ranks and ticks indicating the GSEA walk length.

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

plotEnrichment2 function

<dl><dt>pathways</dt>
<dd>A list of pathways.</dd>
<dt>pwayname</dt>
<dd>The name of the pathway for which to plot enrichment.</dd>
<dt>stats</dt>
<dd>A rank vector obtained from the 'fgsea' package.</dd>
<dt>gseaParam</dt>
<dd>The GSEA walk length parameter. Default is 1.</dd>
<dt>ticksSize</dt>
<dd>The size of the tick marks. Default is 0.2.</dd></dl>

Arguments

Plot Enrichment for a Specific Pathway in fgsea — plotEnrichment2

<dl>

<dt>pathways</dt>
<dd>A list of pathways.</dd>


<dt>pwayname</dt>
<dd>The name of the pathway for which to plot enrichment.</dd>


<dt>stats</dt>
<dd>A rank vector obtained from the 'fgsea' package.</dd>


<dt>gseaParam</dt>
<dd>The GSEA walk length parameter. Default is 1.</dd>


<dt>ticksSize</dt>
<dd>The size of the tick marks. Default is 0.2.</dd>

</dl>

plotEnrichment2: Plot Enrichment for a Specific Pathway in fgsea

Description

Usage

Value

Arguments