quarto-dev / quarto-dev/quarto-cli

Glimma HTML output does not render when embedding via html tag

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#8,978 7 comments 0 reactions 1 assignee View on GitHub

@cderv is already working on this.

Since Apr 14, 2025.

bug
Dominant language
JavaScript
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Description

Bug description

I'm trying to embed the outputs in a .qmd file as follows. Note: There are multiple outputs in HTML widgets, so, don't want to overload the quatro document with it by rendering the code within the document. So, though embedding the final HTML outputs would be easier and cleaner.

I would like to include each .HTML output in a specific tab, tried it as follows, but it did not work. I dont' get an error, but the tab 2 does not render the HTML plot or table.

Steps to reproduce

I have output from Glimma as follows

library(Glimma)
library(DESeq2)

dge <- readRDS(system.file("RNAseq123/dge.rds", package = "Glimma"))

dds <- DESeqDataSetFromMatrix(
  countData = dge$counts,
  colData = dge$samples,
  rowData = dge$genes,
  design = ~group
)
dds <- DESeq(dds, quiet=TRUE)

tab1 <- glimmaMA(dds)
tab1_1 <- glimmaVolcano(dds)
# Tab2
tab2 <- glimmaMA(dds)
tab2_2  <- glimmaVolcano(dds)

htmlwidgets::saveWidget(tab1, "tab1.html")
htmlwidgets::saveWidget(tab1_1, "tab1_1.html")
htmlwidgets::saveWidget(tab2, "tab2.html")
htmlwidgets::saveWidget(tab2_2, "tab2_2.html")

Below is my example quatro document.

---
title: "test"
format: html
editor: visual
---

::: {.panel-tabset}
## Tab 1
Tab content

```{=html}
<iframe width="780" height="500" src="tab1.html" title="tab1"></iframe>
```

sub content  

```{=html}
<iframe width="780" height="500" src="tab1_1.html" title="tab1_1"></iframe>
```

## Tab 2
Tab content

```{=html}
<iframe width="780" height="500" src="tab2.html" title="tab2"></iframe>
```

sub content  

```{=html}
<iframe width="780" height="500" src="tab2_2.html" title="tab2_2"></iframe>
```
:::

 


Expected behavior

Should show the same output as tab1

Actual behavior

Does not display the html widget in 2nd tab.

Your environment
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.3

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] DESeq2_1.42.0               SummarizedExperiment_1.32.0 Biobase_2.62.0             
 [4] MatrixGenerics_1.14.0       matrixStats_1.2.0           GenomicRanges_1.54.1       
 [7] GenomeInfoDb_1.38.6         IRanges_2.36.0              S4Vectors_0.40.2           
[10] BiocGenerics_0.48.1         edgeR_4.0.16                limma_3.58.1               
[13] Glimma_2.12.0              

loaded via a namespace (and not attached):
 [1] gtable_0.3.4            xfun_0.42               ggplot2_3.5.0           htmlwidgets_1.6.4      
 [5] lattice_0.22-5          vctrs_0.6.5             tools_4.3.2             bitops_1.0-7           
 [9] generics_0.1.3          parallel_4.3.2          tibble_3.2.1            fansi_1.0.6            
[13] pkgconfig_2.0.3         Matrix_1.6-5            lifecycle_1.0.4         GenomeInfoDbData_1.2.11
[17] compiler_4.3.2          statmod_1.5.0           munsell_0.5.0           codetools_0.2-19       
[21] htmltools_0.5.7         RCurl_1.98-1.14         yaml_2.3.8              pillar_1.9.0           
[25] crayon_1.5.2            ellipsis_0.3.2          BiocParallel_1.36.0     DelayedArray_0.28.0    
[29] abind_1.4-5             tidyselect_1.2.0        locfit_1.5-9.8          digest_0.6.34          
[33] dplyr_1.1.4             fastmap_1.1.1           grid_4.3.2              colorspace_2.1-0       
[37] cli_3.6.2               SparseArray_1.2.4       magrittr_2.0.3          S4Arrays_1.2.0         
[41] utf8_1.2.4              scales_1.3.0            rmarkdown_2.25          XVector_0.42.0         
[45] evaluate_0.23           knitr_1.45              rlang_1.1.3             Rcpp_1.0.12            
[49] glue_1.7.0              BiocManager_1.30.22     renv_1.0.5              rstudioapi_0.15.0      
[53] jsonlite_1.8.8          R6_2.5.1                zlibbioc_1.48.0  
Quarto check output
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.1: OK
      Dart Sass version 1.55.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.3.450
      Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.9.6
      Path: /Library/Developer/CommandLineTools/usr/bin/python3
      Jupyter: (None)

      Jupyter is not available in this Python installation.
      Install with python3 -m pip install jupyter

(/) Checking R installation...........Warning message:
In chonly && is.symbol(arg) : invalid 'x' type in 'x && y'
[✓] Checking R installation...........OK
      Version: 4.3.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Users/user.3/Library/CloudStorage/OneDrive/test_analysis/renv/library/R-4.3/aarch64-apple-darwin20
        - /Users/user.3/Library/Caches/org.R-project.R/R/renv/sandbox/R-4.3/aarch64-apple-darwin20/ac5c2659
      knitr: 1.45
      rmarkdown: 2.25

[✓] Checking Knitr engine render......OK

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