Using quarto for bioinformatics reporting

Rene Welch
CISR / onglab / UW Madison

2025-05-20

what is quarto?

A bad why of pronouncing 4?

why quarto?

• we had used rmarkdown or variations for a while

• it works with other languages: Python, Julia, …

• it allows to render many things:

  • books
  • websites
  • manuscripts

• mostly because the notation is cleaner

quarto notation I

Instead of adding everything inside the header ‘```{r}’ header, it looks like:

```{r}
#| label: "test-plot"
#| include: true
#| echo: "fenced"
#| eval: false

library(magrittr)
library(tidyverse)
library(ggplot2)

tibble(x = rnorm(20), y = rnorm(20)) |>
  ggplot(aes(x, y)) +
    geom_point()
```

echo: "fenced" gives the code blocks like that

quarto notation II

modifications to the output is done within :::, for example tabs:

::: {.panel-tabset}

## Element 1

## Element 2

:::

revealing slide points incrementally:

::: {.incremental}

 point 1

 point 2

:::

callouts

Using something like:

::: {.callout-important}

# Important message

The results ....

:::

yields:

Important message

The results ….

add html files inside your document

• For example to add slides or MultiQC reports into the documents

add html files inside your document

In the yaml header

---
resources:
  - "path/to/multiqc_report.html"
---

In a chunk

```{r}
#| label: "multiqc-report"
#| echo: "fenced"
#| eval: false

knitr::include_url("path/to/multiqc_report.html",
  height = "720px")
```

It looks as in: https://biostat.wisc.edu/~rwelch/onglab/albertini/SatTCR_report/qc.html#multiqc-report

using templates with quarto

• used when a task is repeated many times, and want the same plot / analysis for many elements

• it is done in 3 steps

step 1: render function

```{r}
#| label: "setup-motif"
#| include: true
#| echo: "fenced"
#| eval: false

render_file <- function(motif) {

  res = knitr::knit_expand(
    file = "template_motif.qmd",
    motif = motif,
    motif2 = snakecase::to_snake_case(motif))
  res

}

unparsed <- map(pdata$motif, render_file)
```

the template file looks as

step 2: parse the template

```{r}
#| label: "setup-motif-p2"
#| include: true
#| echo: "fenced"
#| eval: false

unparsed <- map(pdata$motif, render_file)
parsed <- knitr::knit_child(text = unlist(unparsed),
   envir = rlang::env(
    pdata = pdata
  ))    
```

step 3: evaluate the code in the main document

In summary:

• step 1: replaces the “motif” word, wherever it says “{{motif}}”
• step 2: added pdata into the environment that is evaluated in the template
• step 3: parse the results

gt

gt: https://gt.rstudio.com/

gt example:

```{r}
#| label: "model-example"
#| include: true
#| echo: "fenced"
#| eval: false

  int_model |>
    tidy_zeroinfl() |>
    mutate(
      component = if_else(component == "conditional", "count", "zero")) |>
    filter(term != "(Intercept)") |>
    select(- df.error, - original_term, -statistic) |>
    mutate(
      term = case_when(
        term == "treatmenttreat" ~ "treatment",
        term == "conditionB16_mixed" ~ "mixed dose",
        TRUE ~ "interaction")) |>
    gt::gt(
      groupname_col = "component", rowname_col = "term") |>
      gt::fmt_number(one_of(c("estimate", "std.error"))) |>
      gt::fmt_number(starts_with("conf")) |>
      gt::fmt_percent("conf.level") |>
      gt::fmt_scientific("p.value") |>
      gt::cols_add(
        psgn = if_else(p.value <= 0.05, "*", "")) |>
      gt::cols_label(psgn = "")
```

gt example:

• this is a small table: for larger tables opt_interactive can allow for multiple pages

reproducible documents with targets

your own website

gifs in quarto

gifs in quarto

how to add cats in quarto

with extensions

To get this cat:

1. Install the fontawesome quarto extension:
   quarto add quarto-ext/fontawesome

2. Write {{ < fa cat size=5x > } }

https://github.com/quarto-ext/fontawesome

other extensions: https://quarto.org/docs/extensions/

with images and knitr

find a cat image

• open image in new tab
• copy link of new image

with images and knitr

• Code
• Cat

```{r}
#| label: "cat-git2"
#| include: true
#| echo: "fenced"
#| eval: false

knitr::include_url("https://i.giphy.com/VbnUQpnihPSIgIXuZv.webp", height = "600px")
```

extra materials from people who know more than me

1. Quarto authoring webinar https://jthomasmock.github.io/quarto-2hr-webinar/

2. Stephen Turner’s blog https://blog.stephenturner.us/p/quarto-books

3. Quarto’s gallery https://quarto.org/docs/gallery/

4. Using python and R together https://nrennie.rbind.io/blog/combining-r-and-python-with-reticulate-and-quarto/

other tricks?