highlight_genes: Add Highlights for Genes on a Phylogenetic Tree

In TransProR: Analysis and Visualization of Multi-Omics Data

Add Highlights for Genes on a Phylogenetic Tree

Description

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

Usage

highlight_genes(ggtree_obj, genes_to_highlight, hilight_extend = 18)

Arguments

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

Value

A 'ggtree' object with added highlights for specified genes.

Examples

plot_file <- system.file("extdata", "tree_plot.rds", package = "TransProR")
p2_plot <- readRDS(plot_file)

selected_genes_deseq2_file <- system.file("extdata",
                                          "selected_genes_deseq2.rds",
                                          package = "TransProR")
selected_genes_deseq2 <- readRDS(selected_genes_deseq2_file)

Diff_deseq2_file <- system.file("extdata", "Diff_deseq2.rds", package = "TransProR")
Diff_deseq2 <- readRDS(Diff_deseq2_file)

result_deseq2 <- gene_color(selected_genes_deseq2, Diff_deseq2, "#0000EE", "#fc4746")

add_gene_highlights_p3 <- highlight_genes(p2_plot, result_deseq2, hilight_extend = 26)

TransProR documentation built on April 4, 2025, 3:16 a.m.