rmd template

gistfile1.rmd

---
title: "<title>"
author: "<name>"
date: 'Compiled: `r format(Sys.Date(), "%B %d, %Y")`'
editor_options: 
  chunk_output_type: console
output:
  html_document:
    keep_md: true
engine: knitr
---

```{r setup, include=FALSE}
# Set global R options for efficient output
options(
  max.print = 500,   # Reduced limit for printing
  scipen = 10        # Moderate scientific notation suppression
)

# Set knitr chunk options for compact output
knitr::opts_chunk$set(
  echo = TRUE,       # Show code
  message = FALSE,   # Suppress package messages
  warning = FALSE,   # Suppress warnings
  collapse = TRUE,   # Combine code and output
  comment = "#>",    # Standard comment for output
  dpi = 300,         # Balanced resolution for web
  out.width = "100%" # Full-width plots
)

# Set seed for reproducibility
set.seed(123)
```

```{r load-libraries, message=TRUE, warning=TRUE}
library(here)         # File path management
library(this.path)    # Retrieve its own path without the explicit need to write it elsewhere
library(tinytable)    # For saving tables as images
library(tidyverse)    # Data manipulation, CSV reading, and plotting (includes dplyr, tidyr, readr, ggplot2)
library(ggrepel)      # Non-overlapping labels
library(scales)       # Label formatting
library(patchwork)    # Combine multiple plots
```

```{r configuration}

# File Paths
# Define the output directory for results
output_dir <- here("analysis_results", gsub(
  "\\.([^\\.]+)$", # change .<ext> 
  "_\\1",          # to _<ext>
  basename(this.path())
))
# Define the path to the directory containing the processed Excel files
data_dir <- here("raw_data")

# Visualization (optimized for google slides)
plot_width <- 8.2 # Inches
plot_height <- 4.8 # Inches
plot_units <- "in"
plot_res <- 300 # dpi
padj_threshold <- 0.05 # Significance threshold
```

# --- Start working ---

```{r}

```


```{r}
plot_file <- file.path(output_dir, "plot_ggplot.png")

# <ggplot2 script>

# ggsave(
#   plot_file,
#   plot = plot_gg,
#   width = plot_width,
#   height = plot_height,
#   units = plot_units,
#   dpi = plot_res,
#   bg = 'white'
# )
```