highlight_genes

This function adds highlights for specified genes on a phylogenetic tree object.

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

highlight_genes function

<dl><dt>ggtree_obj</dt>
<dd>A ggtree object representing the phylogenetic tree.</dd>
<dt>genes_to_highlight</dt>
<dd>A data frame containing gene names and corresponding colors to highlight.</dd>
<dt>hilight_extend</dt>
<dd>Numeric value indicating the extension length for highlights.</dd></dl>

Arguments

Add Highlights for Genes on a Phylogenetic Tree — highlight_genes

<dl>

<dt>ggtree_obj</dt>
<dd>A ggtree object representing the phylogenetic tree.</dd>


<dt>genes_to_highlight</dt>
<dd>A data frame containing gene names and corresponding colors to highlight.</dd>


<dt>hilight_extend</dt>
<dd>Numeric value indicating the extension length for highlights.</dd>

</dl>

highlight_genes: Add Highlights for Genes on a Phylogenetic Tree

Description

Usage

Value

Arguments

Examples