rmd-formatting

name	rmd-formatting
description	R Markdown formatting patterns: chunk display strategies (include=FALSE + inline R vs results='asis'), table rendering with knitr::kable, header hierarchy with tabsets, downloadable file embedding, and what to avoid (cat/print in visible chunks).

R Markdown Report Formatting

Core principle

Never use cat() or print() in visible chunks for user-facing output — it renders as monospace code blocks with ## prefixes. Use include=FALSE + inline R, or results='asis'.

Pattern 1: Simple statistics (preferred)

# Hidden computation
```{r, include=FALSE}
n_cells <- ncol(obj)
n_genes <- nrow(obj)

Dataset: r format(n_cells, big.mark = ",") cells · r format(n_genes, big.mark = ",") genes

## Pattern 2: Tables

```r
```{r, include=FALSE}
sample_counts <- as.data.frame(table(obj$Sample))
colnames(sample_counts) <- c("Sample", "Cells")

knitr::kable(sample_counts)

## Pattern 3: results='asis' (mixed compute + display in one chunk)

When a chunk must compute AND render text (e.g., QC loops):

**Required global setup:**
```r
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE, comment = "")

Rules for `results='asis'` chunks:
1. `cat("text\n")` for plain text — renders as markdown
2. Tables: `knitr::kable(df, format = "markdown") |> cat(sep = "\n")` — NOT `print(df)`
3. End text blocks with `\n\n` for paragraph spacing

```r
```{r qc-summary, results='asis'}
n_pass <- sum(obj$pass_qc)
n_total <- ncol(obj)
cat(sprintf("**%d / %d cells pass QC (%.0f%%)**\n\n", n_pass, n_total, 100*n_pass/n_total))

tbl <- as.data.frame(table(obj$CellType, obj$pass_qc))
knitr::kable(tbl, format = "markdown") |> cat(sep = "\n")

## Pattern 4: Downloadable files

```r
# In a chunk with results='asis':
xfun::embed_file("path/to/file.xlsx", name = "output.xlsx", text = "Download Results (Excel)")

Header hierarchy

• # {.tabset} — FIRST tabset only (level 1)
• ## Tab Name — tabs within the first tabset; also all subsequent section headers
• ## {.tabset} — any subsequent tabsets (level 2)
• ### — subsections within tabs, or tabs of a level-2 tabset
• #### — sub-subsections

Start reports with a 1–2 sentence project description, then # {.tabset} directly. No "Executive Summary" or "Data Loading" sections at the top — data loading goes inside the first tab.

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE, comment = "")

Brief project description here.

{.tabset}

Data Loading

Analysis

Subsection

Session Information

Quick reference

Situation	Use
Simple stats (1–3 values)	include=FALSE + inline R
Complex/conditional text	results='asis' + cat()
Tables (always)	knitr::kable()
Never	print(), print(table()) in visible chunks