I just noticed how the latest build(s) of quarto renders mermaid diagrams as png images instead of the natively supported ` ``` mermaid ` blocks when using the gfm format. This feature appears to have been removed in c4af1a1bed2cf448cb4e10d0d0dcae246a8c0b5e.

This breaks several mermaid functionalities, such as being able to use nodes in the diagram to link to other sections in the document -- shown in Figures 1 and 2.

Why was this feature removed in c4af1a1bed2cf448cb4e10d0d0dcae246a8c0b5e? Can it be parameterised so I have the option of not turning it into a PNG? Or at least allow me to turn it into an SVG?

Kind regards,
Robrecht

---


Example:

<div class="column-page">

<div id="fig-architecture">

<p>

``` mermaid

flowchart LR
  Raw[Raw\nreads]
  Counts[Raw\ncounts]
  SS[Unimodal\nsample]
  MS[Unimodal\nmulti-sample]
  MM[Multi-modal\nmulti-sample]
  Ingestion[/Ingestion/]
  Preproc1[/Single-sample\nprocessing/]
  Preproc2[/Multi-sample\nprocessing/]
  Integration[/Integration/]

  Raw --- Ingestion --> Counts --- Preproc1 --> SS --- Preproc2 --> MS --- Integration --> MM

  Ingestion -.-|"- Demux.\n- Mapping"| Ingestion
  Preproc1 -.-|"- Count QC\n- Doublet calling\n- Ambient RNA\n- Gatekeeper"| Preproc1
  Preproc2 -.-|"- Normalisation\n- Feature filtering\n- Feature selection\n- Batch correction?\n- Dim. red.?"| Preproc2
  Integration -.-|"- Dim. red.\n- Data integration"| Integration

  linkStyle 8,9,10,11 stroke:#fff,stroke-width:0px,text-align:left;

  click Ingestion "https://github.com/openpipelines-bio/openpipeline/blob/e1d4e6675f46e10805fc9f5bbc47917e3c16ea64/docs/design.md#ingestion"

```

</p>

Figure 1: Before commit c4af1a1bed2cf448cb4e10d0d0dcae246a8c0b5e. Notice how clicking the 'Ingestion' box takes you to the section documenting the 'Ingestion' pipeline.

</div>

</div>

<div class="column-page">

<div id="fig-architecture">

<p>

<img src="https://raw.githubusercontent.com/openpipelines-bio/openpipeline/e1d4e6675f46e10805fc9f5bbc47917e3c16ea64/docs/design_files/figure-gfm/mermaid-figure-1.png" data-fig-pos="H"
style="width:13.97803in;height:2in" />

</p>

Figure 2: After commit c4af1a1bed2cf448cb4e10d0d0dcae246a8c0b5e. This PNG does not integrate well with a dark themed github and does not allow for linking to other pages.

</div>

</div>
cscheid
2022-05-30T18:00:06Z
rcannood
closed
Mermaid in gfm turned into PNG
https://github.com/quarto-dev/quarto-cli/issues/1021