bio-reporting-rmarkdown-reports

Version Compatibility

Reference examples tested with: rmarkdown 2.25+, knitr 1.45+, DESeq2 1.42+, ggplot2 3.5+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

R Markdown Reports

"Create an R Markdown report" → Write reproducible R-based documents combining code chunks, results, and narrative that render to HTML/PDF/Word.

• R: rmarkdown::render('report.Rmd'), or Knit button in RStudio

Basic Document Structure

---
title: "RNA-seq Analysis Report"
author: "Your Name"
date: "`r Sys.Date()`"
output:
  html_document:
    toc: true
    toc_float: true
    code_folding: hide
    theme: cosmo
---

Setup Chunk

```{r setup, include=FALSE}
knitr::opts_chunk$set(
    echo = TRUE,
    message = FALSE,
    warning = FALSE,
    fig.width = 10,
    fig.height = 6,
    fig.align = 'center'
)
library(tidyverse)
library(DESeq2)
library(pheatmap)
```

Code Chunk Options

```{r analysis, echo=TRUE, results='hide'}
# echo: show code
# results: 'hide', 'asis', 'markup'
# include: FALSE hides chunk entirely
# eval: FALSE shows code but doesn't run
# cache: TRUE caches results
```

Parameterized Reports

---
title: "Sample Report"
params:
  sample_id: "sample1"
  count_file: "counts.csv"
  fdr_threshold: 0.05
---

```{r}
counts <- read.csv(params$count_file)
sample <- params$sample_id
fdr <- params$fdr_threshold
```

# Render with parameters
rmarkdown::render('report.Rmd', params = list(sample_id = 'sample2', fdr_threshold = 0.01))

# Batch render
samples <- c('sample1', 'sample2', 'sample3')
for (s in samples) {
    rmarkdown::render('report.Rmd', params = list(sample_id = s),
                       output_file = paste0(s, '_report.html'))
}