R Using Anaconda Evnironment

Step 1: Installing R Additional Package with Anaconda

To install R additional packages with Anaconda, run below command in the SSH terminal (CLI), for tutorial in accessing CLI, please refer to Shell Access and Useful Command

# Load Anaconda Environment Module
$ module load anaconda

# Add conda-forge Channels
$ conda config --add channels conda-forge

# Create Anaconda Virtual Environment
$ conda create –n <environment name> <packages to install>

# Create Anaconda Virtual Environment (Example)
$ conda create -n R_test_env r-base=4.3 r-cairo r-gifi

# Install Missing Package (Example)
$ ${CONDA_ENV_PATH}/R_test_env/bin/Rscript -e "install.packages(c('MPsychoR'), repos='https://cran.r-project.org')"

# Purge Module
$ module purge

Step 2: Prepare R Program Source Code

Example source code path -> /home/$USER/job_template/R/MPsychoR_test.R

# Load libraries
library(MPsychoR)
library(Gifi)
library(Cairo)
# Load the built-in dataset
data("zareki")

# Extract subtraction items (columns containing "subtr")
zarsub <- zareki[, grep("subtr", colnames(zareki))]

# Perform nonlinear principal component analysis
prinzar <- princals(zarsub)

# ---------------------------------------------------------
# 1. Export the loadings plot to PNG using Cairo
# ---------------------------------------------------------
CairoPNG(filename = "zareki_subtraction_loadings.png",
    width = 800, height = 600, dpi = 150, bg = "white")

plot(prinzar, main = "Zareki Subtraction Items Loadings Plot")

dev.off()

cat("Loadings plot saved as 'zareki_subtraction_loadings.png'\n in directory:", getwd(), "\n")

# ---------------------------------------------------------
# 2. Export the text results (summary) as a PNG
# ---------------------------------------------------------
# Capture the printed output
output_text <- capture.output(print(prinzar))

CairoPNG(filename = "zareki_subtraction_results.png",
    width = 1000, height = 1400, dpi = 150, bg = "white")

# Create an empty plot and add text
plot.new()
par(mar = c(2, 2, 3, 2))  # Small margins
title(main = "Princals Results: Zareki Subtraction Items",
  cex.main = 1.6, font.main = 2)

# Render the captured text on the canvas
text(x = 0.02, y = 0.98,
  labels = paste(output_text, collapse = "\n"),
  adj = c(0, 1),   # Left- and top-aligned
  cex = 0.85,      # Text size (adjust if needed)
  family = "mono") # Monospace font for clean alignment

dev.off()

cat("Text results saved as 'zareki_subtraction_results.png'\n in directory:", getwd(), "\n")

Step 3: Prepare Job Template Script

Pre-configured template script path -> /home/$USER/job_template/slurm_job/MPsychoR_test_conda.sh

#!/bin/bash
#SBATCH --job-name=MPsychoR_test_conda ## Job Name
#SBATCH --partition=shared_cpu ## Partition for Running Job
#SBATCH --nodes=1 ## Number of Compute Node
#SBATCH --ntasks-per-node=1 # Number of Task per Compute Node
#SBATCH --cpus-per-task=2 ## Number of CPU per task
#SBATCH --time=60:00 ## Job Time Limit (i.e. 60 Minutes)
#SBATCH --mem=10GB ## Total Memory for Job
#SBATCH --output=./%x%j.out ## Output File Path
#SBATCH --error=./%x%j.err ## Error Log Path

## Initiate Environment Module
source /usr/share/modules/init/profile.sh

## Reset the Environment Module components
module purge

## Load Module
module load anaconda

## Run user command in conda environemnt
## Do not use conda activate command, use absolute path instead
${CONDA_ENV_PATH}/R_test_env/bin/Rscript \
/home/${USER}/job_template/R/MPsychoR_test.R

## Clear Environment Module components
module purge

Step 4: Create Template (Web Interface Feature)

To submit HPC via web interface a job template is required, details please refer to: HPC Job Template For Job submission via CLI Terminal, please skip this step.

Step 5: Submit HPC Job

Guides for submitting HPC job, please refer to: HPC Job Submission

Step 6: Remove user’s Conda (R) environment (Optional)

# Remove user’s Conda (R) environment
$ rm –rf /home/$USER/.conda/envs/<environment name>

# Remove user’s Conda (R) environment (Example)
$ rm –rf /home/$USER/.conda/envs/R_test_env