Installation

This section covers the installation and setup of the TRIAGE R package. The TRIAGE R package requires both R and Python dependencies. Follow these steps to set up the environment and install the package.

R Dependencies

Install the required R packages:

install.packages("reticulate")
install.packages("data.table")
install.packages("pheatmap")

Additional Packages for compareGO

To enable the compareGO function, the following R packages are required:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install(c("clusterProfiler", "enrichplot"))
install.packages(c("dplyr", "ggplot2", "reshape2"))

These packages are only required for compareGO, which performs GO enrichment analysis on gene lists. Note it also requires an organism-specific annotation database (e.g., org.Hs.eg.db for human), which can be installed with:

BiocManager::install("org.Hs.eg.db")

Common options include org.Hs.eg.db for humans, org.Mm.eg.db for mice, and org.Rn.eg.db for rats (default: org.Hs.eg.db). For additional species databases, see the [Bioconductor Annotation Packages](https://bioconductor.org/packages/release/BiocViews.html#___OrgDb).

Python Environment Setup

Install Python modules within R using the reticulate package. It’s recommended to manage Python dependencies in a separate environment.

library(reticulate)
# Note: any Python with version >=3.9 works. Here we install Python version 3.9.5 as an example.
reticulate::install_python(version = '3.9.5')
reticulate::py_install("pandas", envname = "r-reticulate")
reticulate::py_install("numpy", envname = "r-reticulate")
reticulate::py_install("scipy", envname = "r-reticulate")
reticulate::py_install("matplotlib", envname = "r-reticulate")
reticulate::py_install("requests", envname = "r-reticulate")
reticulate::py_install("scikit-learn", envname = "r-reticulate")
reticulate::py_install("seaborn", envname = "r-reticulate")

Knowledge Base

When using the reticulate package in R to install Python modules, it is important to understand how reticulate::py_install manages the installation of these modules. Below are key points to consider:

  • Intelligent Installation: The reticulate::py_install function is designed to intelligently manage Python modules within your specified Python environment. It checks whether the required modules are already installed in the targeted environment.

  • No Redundant Installation: If a module is already installed in the given environment, py_install will not attempt to reinstall it. This avoids redundant installation and saves time, especially when setting up the environment for the first time or in a new session.

  • Specified Environment: You can specify the environment where you want the modules to be installed. This is done using the envname parameter in the py_install function. For instance, reticulate::py_install(“pandas”, envname = “r-reticulate”) will install the pandas module in the r-reticulate environment.

In future R sessions, activate the r-reticulate environment:

library(reticulate)
use_virtualenv("r-reticulate", required = TRUE)

Installing TRIAGE R Package

  1. Download the TRIAGE R package (e.g., TRIAGE_1.1.5.tar.gz) from the GitHub repository: https://github.com/Qiongyi/TRIAGE_R_Package

  2. Install the TRIAGE R package from the source file:

install.packages("path/to/TRIAGE_1.1.5.tar.gz", repos = NULL, type = "source")
library(TRIAGE)