quarto-dev / quarto-dev/quarto-cli
Glimma HTML output does not render when embedding via html tag
@cderv is already working on this.
Since Apr 14, 2025.
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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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