gene_highlights

This function enhances a `ggtree` plot by adding highlights for specific genes. It adds both a semi-transparent fan-shaped
highlight and a point at the node corresponding to each gene. Colors for each gene can be customized.

A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10.1186/s13059-022-02648-4>), providing flexible and robust approaches to RNA-Seq data analysis. For more information, refer to the package vignettes and related publications.

Dongyue Yu

TransProR

Analysis and Visualization of Multi-Omics Data

gene_highlights function

<dl><dt>ggtree_obj</dt>
<dd>A ggtree object to which the highlights will be added.</dd>
<dt>genes_to_highlight</dt>
<dd>A data frame containing genes and their corresponding colors.</dd>
<dt>hilight_extend</dt>
<dd>Integer, the extension of the highlight fan in degrees.</dd></dl>

Arguments

Add gene highlights to a ggtree object — gene_highlights

<dl>

<dt>ggtree_obj</dt>
<dd>A ggtree object to which the highlights will be added.</dd>


<dt>genes_to_highlight</dt>
<dd>A data frame containing genes and their corresponding colors.</dd>


<dt>hilight_extend</dt>
<dd>Integer, the extension of the highlight fan in degrees.</dd>

</dl>

gene_highlights: Add gene highlights to a ggtree object

Description

Usage

Value

Arguments

Examples