code-style.md

Code Style & Conventions

R

• Use tidyverse style: snake_case for objects and functions
• Limit lines to 100 characters
• Use <- for assignment, not =
• Use the package conflicted to resolve package conflicts
• Use # ---- as section delimiters
• Always use ggpubr::theme_pubr() for plot themes

Example:

# Data processing ----
processed_data <- raw_data %>%
  dplyr::filter(quality > threshold) %>%
  dplyr::mutate(log_value = log10(value + 1))

Python

• Follow PEP 8 with 100-character line limit
• Use snake_case for functions and variables, PascalCase for classes
• Use type hints where reasonable
• Format with Black or equivalent

Example:

def calculate_statistics(data: pd.DataFrame) -> dict:
    """Calculate summary statistics."""
    return {
        "mean": data.mean(),
        "std": data.std(),
    }

Shell Scripts

• Use #!/bin/bash header
• Comment non-obvious sections
• Use meaningful variable names in UPPER_CASE
• Check for errors: set -e at top of script

Example:

#!/bin/bash
set -e

INPUT_FILE="$1"
OUTPUT_DIR="./processed"