GraphViz as figure when generated by R code

[mike-lawrence]

Description

I've seen the docs on hand-expressed Graphviz diagrams, but my diagrams will all be auto-generated by R code via the DiagrammeR package and I can't seem to work out how to have them render in my quarto document.

This works in Rstudio, showing the diagram in the Viewer pane, but doesn't render to the html document:

DiagrammeR::render_graph(my_dgr_graph_obj)

This adds the dot code to the document, but doesn't render

cat(DiagrammeR::generate_dot(my_dgr_graph_obj))

[rich-iannone]

The rendering seems to work for me. Here's my .qmd document:

---
output: html
---


```{r}
library(DiagrammeR)

create_graph() %>%
  add_node() %>%
  add_node() %>%
  add_edge(from = 1, to = 2) %>%
  render_graph()
```

My output:

Which version of DiagrammeR are you using?

[mike-lawrence]

I'm using v 1.0.10.9000

When I use the render_graph() method, it shows in Rstudio fine but when I render to html I get the error:

Error in `add_html_caption()`:
! unused argument (xfun::grep_sub("^[^<]*<[^>]+aria-labelledby[ ]*=[ ]*\"([^\"]+)\".*$", "\\1", x))
Backtrace:
  1. global .main()
  2. execute(...)
  3. rmarkdown::render(...)
  4. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  5. knitr:::process_file(text, output)
     ...
 14. sew(res, options)
 15. knitr:::sew.list(x, options, ...)
 16. base::lapply(x, sew, options, ...)
 17. FUN(X[[i]], ...)
 18. knitr:::sew.knit_asis(x, options, ...)
Execution halted

in case it helps, here's the dot code from generate_dot():

digraph {

graph [layout = 'dot',
       outputorder = 'edgesfirst',
       bgcolor = 'white',
       rankdir = 'UD']

node [fontname = 'Helvetica',
      fontsize = '10',
      shape = 'circle',
      fixedsize = 'true',
      width = '0.5',
      style = 'filled',
      fillcolor = 'aliceblue',
      color = 'gray70',
      fontcolor = 'gray50']

edge [fontname = 'Helvetica',
     fontsize = '8',
     len = '1.5',
     color = 'gray80',
     arrowsize = '0.5']

  '6' [label = 'data', fontcolor = 'black', color = '#FFD92F', fillcolor = '#FFD92F'] 
  '7' [label = 'transformed
data', fontcolor = 'black', color = '#A6D854', fillcolor = '#A6D854'] 
  '8' [label = 'parameters', fontcolor = 'black', color = '#E78AC3', fillcolor = '#E78AC3'] 
  '9' [label = 'transformed
parameters', fontcolor = 'black', color = '#8DA0CB', fillcolor = '#8DA0CB'] 
  '10' [label = 'model', fontcolor = 'black', color = '#FC8D62', fillcolor = '#FC8D62'] 
  '11' [label = 'generated
quantities', fontcolor = 'black', color = '#66C2A5', fillcolor = '#66C2A5'] 
  '12' [label = 'data', fontcolor = 'transparent', color = 'transparent', fillcolor = 'transparent'] 
  '13' [label = 'transformed
data', fontcolor = 'transparent', color = 'transparent', fillcolor = 'transparent'] 
  '14' [label = 'parameters', fontcolor = 'transparent', color = 'transparent', fillcolor = 'transparent'] 
  '15' [label = 'transformed
parameters', fontcolor = 'transparent', color = 'transparent', fillcolor = 'transparent'] 
  '16' [label = 'model', fontcolor = 'transparent', color = 'transparent', fillcolor = 'transparent'] 
  '17' [label = 'generated
quantities', fontcolor = 'transparent', color = 'transparent', fillcolor = 'transparent'] 
  '2' [label = 'prob_success', fontcolor = 'black', color = '#E78AC3', fillcolor = '#E78AC3'] 
  '3' [label = 'obs', fontcolor = 'black', color = '#FFD92F', fillcolor = '#FFD92F'] 
  '4' [label = 'bernoulli', fontcolor = 'black', color = '#FC8D62', fillcolor = '#FC8D62'] 
  '5' [label = 'beta', fontcolor = 'black', color = '#FC8D62', fillcolor = '#FC8D62'] 
'5'->'2' [color = 'gray'] 
'4'->'3' [color = 'red'] 
'2'->'4' [color = 'gray'] 
'6'->'7' [color = 'transparent'] 
'7'->'8' [color = 'transparent'] 
'8'->'9' [color = 'transparent'] 
'9'->'10' [color = 'transparent'] 
'10'->'11' [color = 'transparent'] 
'12'->'13' [color = 'transparent'] 
'13'->'14' [color = 'transparent'] 
'14'->'15' [color = 'transparent'] 
'15'->'16' [color = 'transparent'] 
'16'->'17' [color = 'transparent'] 
}

[mcanouil]

The error about add_html_caption() has been fixed in Quarto 1.3 (it's related to knitr 1.43).
Which version are you using?

[mike-lawrence]

Thanks @mcanouil ! Updatingn to the latest release (seems Rstudio is behind) fixed it!