Implementing dynamic figure captions for multiple heatmaps within a loop in a Quarto document.

[Liu499-create]

---

Issue Description

Background

I am using Quarto to generate a report where I need to dynamically generate multiple heatmaps within a single R code block using the purrr::iwalk loop. My goal is to set dynamic figure captions for each heatmap based on variables within the loop. I tried using the fig-cap parameter in combination with the glue::glue function to dynamically generate captions, but this method seems to only work for the first heatmap in the loop and does not support multiple figures within the same loop.

Attempted Solutions

I have tried the following methods to achieve dynamic figure captions:

1. Using glue::glue within fig-cap to reference loop variables, hoping to generate different captions for each figure. For example:

   #| fig-cap: !expr glue::glue("{names(descrips)}pheatmap")

   This method only works for the first figure in the loop, and captions for subsequent figures do not display correctly.

2. Manually using the cat() function within the loop to output titles. Although this method allows for accurate descriptions, it does not integrate into the properties of the figure files and does not align with my purpose of using fig-cap.

Problem

How can I dynamically set fig-cap for each figure within a loop in a Quarto document? Is there a recommended method or an upcoming feature update that supports this use case?

Expected Solution

I hope to be able to set individual, dynamically generated figure captions in Quarto, especially when using loops or similar dynamic structures. If the current version of Quarto does not support this, I would like to know if there are plans to include this functionality in future updates.

---

the following is my code

#| label: fig-heatmap-and-statistical-description
#| fig-cap: !expr glue::glue("{names(descrips)}, Hierarchical Clustering Heatmaps")
#| results: 'asis'
#| fig-width: 10
#| fig-height: 6

  # Monthly disease list - Complete year/month heatmaps
  pheatmap_df <- dyq_cstd |>
    dyq_complete_yearmonth(analysis_start_year = analysis_start_year, 
      analysis_end_year = analysis_end_year,
      analysis_quarter = analysis_quarter,
      analysis_disease = analysis_disease)

  iwalk(descrips, ~{
      cat("###  ", .y, "\n\n", sep="")

      cat(.x$year_range, .y, " incidence rate remains high. Reported incidence rates are between ", .x$incidence_range, " per 100,000, with an average annual incidence of ", .x$average_incidence, " per 100,000. The highest annual incidence was in ", .x$highest_incidence_year, ", and the lowest was in ", .x$lowest_incidence_year, ", see ", '@fig-key-disease-incidence-combination-chart', "\n\n")

      # Use plot_heatmap to draw the monthly heatmap
      pheatmap_df[[.y]] |> 
        # When save_path is set to NULL, it is used for output in Quarto
        plot_heatmap(.y, save_path=NULL)
      
      cat("\n\n")
        
  })

[mcanouil]

Could you share a small self-contained "working" (reproducible) example to work with, i.e., a complete Quarto document or a Git repository? The goal is to make it as easy as possible for us to recreate your problem so that we can fix it: please help us help you! Thanks.

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````

Additionally and if not already given, please share the output of quarto check within a code blocks (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.

[mcanouil]

Note that this has been discussed in several other threads:

• How to create different sized figures in programmatically-generated markdown sections #11042
• Dynamic table names when using parameters in quarto #11249
• Multiple `gt` tables in a `for()` renders none of the table #10563
• How to dynamically generate sections with headings and print tables #9886
• Struggeling with creating code chunks prgramatically (why not `cat` everthing, and how to include execute options?) #8560
• How do I generate a new Code-Block from a function inside an R-Package? #7887
• Problem with procedural tabset and ggplot #7282
• How do I print data frames in for loop without using print function? #6033

and many more all using the exact same technique, i.e., knitr::knit_child().

as well as several blog posts such as:

• https://mickael.canouil.fr/posts/2023-03-05-quarto-auto-table-crossref/

[Liu499-create]

Thank you very much for your quick answer, but after following the tutorial you gave for setting up knitr::knit_child(), there is now only one problem, and that is WARNING (C:/Program Files/Quarto/share/filters/main.lua:13878) Unable to resolve crossref, I'm sure there is no problem with the tag reference format, I don't know what the problem is, I'm very confused! Here is my code:

#| echo: false
#| output: asis
#| fig-width: 10
#| fig-height: 6
#| eval: true


descrips<-analysis_disease_rates_list |> 
    imap(~{
         年份范围= range(.x$发病年份) |> paste0(collapse="~")
        发病率范围=range(.x$发病率) |> paste0(collapse="~")
           均值= mean(.x$发病率)
           最大发病率_年<-.x$发病年份[which(.x$发病率==max(.x$发病率))] |> paste0(collapse=",")
           最小发病率_年<-.x$发病年份[which(.x$发病率==min(.x$发病率))]|> paste0(collapse=",")
           return(list(年份范围=年份范围,发病率范围=发病率范围,最大发病率_年=最大发病率_年,
           最小发病率_年=最小发病率_年,均值=均值))
    })

# 病种月度完整年月列表-热图
pheatmap_df<- dyq_cstd|>
    dyq_complete_yearmonth(analysis_start_year = 分析开始的年, 
      analysis_end_year =分析的年,
      analysis_quarter = 分析的季度,
      analysis_disease = 分析病种)

cat( sep = "\n\n")
cat(
  sprintf(
    "- `%s` (@fig-%s)",
    str_remove_all(names(descrips)," "),
    str_remove_all(names(descrips)," ")
    ),
    sep = "\n"
    )

cat(sep ="\n\n")
iwalk(descrips,~{

  cat("### ",.y,"\n\n")
  
  cat(.x$年份范围,.y,"发病率维持在高水平。报告发病率在",.x$发病率范围,"/10万之间，年平均发病率为",.x$均值,"/10万，",.x$最大发病率_年,"年发病率最高，",.x$最小发病率_年,"年发病率最低，","见 ", '@fig-重点病种发病率组合图',"\n\n")
  
  # 使用plot_heatmap绘制月度热图
  ph<-pheatmap_df[[.y]]|> 
    # save_path 指定为NULL时用于quarto输出
    plot_heatmap(.y,save_path=NULL)
    cat("\n\n")
    
    cat(sep = "\n", knitr::knit_child(quiet = TRUE, text = c(
      "```{r}",
      "#| echo: false",
      "#| lang: zh",
      sprintf("#| fig-cap: %s",str_remove_all(.y," ")),
      sprintf("#| label: fig-%s",str_remove_all(.y," ")),
      grid::grid.newpage(),
      cat(grid::grid.draw(ph$gtable),"\n\n"),
      "```"
      )))
      })
```

[mcanouil]

Sorry but there is no way we can use your complex, not English, and not reproducible code.

Could you share a small self-contained "working" (reproducible) example to work with, i.e., a complete Quarto document or a Git repository? The goal is to make it as easy as possible for us to recreate your problem so that we can fix it: please help us help you! Thanks.

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````

Additionally and if not already given, please share the output of quarto check within a code blocks (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.

[Liu499-create]

I would love to use quarto, and would love to cooperate with you guys, but this QMD file I have contains too many of my custom functions, and is also very cumbersome, maybe looking forward to be inspired by the community is a good way, thank you very much for your reply!

[Liu499-create]

The problem is solved, it takes me 16 hours, thank you very much. I write some to make it usefull.

firstly,knit_child is a good idea, but it can not solve all the problem, but U give me inspire so much. so that I can solve the issue.

secondly, my Unknown quantity fig shown was strange,Cross referencing is invalid, because its a pheathot object, I try Direct use,
but I can not do it. maybe due to the grid system is unfriendly to quarto.Unable to capture fig-cap,label.

finally I use knit_child insert these pig by iwalk,its successfull !!! its so cool, quarto is a Magical tools!