create_base_plot: Create a base plot with gene expression data on a...

In TransProR: Analysis and Visualization of Multi-Omics Data

Create a base plot with gene expression data on a phylogenetic tree

Description

This function creates a base plot using 'ggtree' and 'ggtreeExtra' libraries, adding gene expression data as colored tiles to the plot. It allows for dynamic coloring of the genes and includes adjustments for alpha transparency based on the expression value.

Usage

create_base_plot(p, data, gene_colors, gene_label = "Gene")

Arguments

p	A ggtree plot object to which the data will be added.
data	A data frame containing gene expression data with columns for Samples, Genes, and Values.
gene_colors	A named vector of colors for genes.
gene_label	A character string used as a label in the legend for the genes. Default is "Gene".

Value

A 'ggtree' plot object with the gene expression data added.

Examples

# Check and load required packages
if (requireNamespace("ggtreeExtra", quietly = TRUE) &&
 requireNamespace("ggplot2", quietly = TRUE)) {
  library(ggtreeExtra)
  library(ggplot2)

  file_path <- system.file("extdata", "p_tree_test.rds", package = "TransProR")
  p <- readRDS(file_path)

  # Create gene expression data frame
  expression_data <- data.frame(
    Sample = rep(c("Species_A", "Species_B", "Species_C", "Species_D"), each = 5),
    Gene = rep(paste0("Gene", 1:5), times = 4),
    Value = runif(20, min = 0, max = 1)  # Randomly generate expression values between 0 and 1
  )

  # Define gene colors (named vector)
  gene_colors <- c(
    Gene1 = "#491588",
    Gene2 = "#301b8d",
    Gene3 = "#1a237a",
    Gene4 = "#11479c",
    Gene5 = "#0a5797"
  )

  # Call create_base_plot function to add gene expression data
  p <- create_base_plot(p, expression_data, gene_colors)
} else {
  message("Required packages 'ggtreeExtra' and 'ggplot2' are not installed.")
}

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