Rendering Glimma plots after knitting

[joseale2310]

Hi!

I am trying to create an html report using knit from RStudio. The plot works completely fine in the Rmarkdown, but when trying to knit the document, the plot loses several features, like the table and count plot (although the document leaves the space necessary for the table). I can still hover the genes and check their values, but clicking does not do anything.

These are my markdown options

--- 
knit: (function(inputFile, encoding) { 
      rmarkdown::render(inputFile,
                        encoding=encoding,
                        output_format='all',
                        output_dir='./reports/')})
output:
  # To create PDF report, uncomment below
  #pdf_document:
  #  toc: yes
  html_document:
    number_sections: yes
    theme: yeti
    toc: yes
    toc_float: yes
    df_print: paged
    dev: png
---

I am not sure if there is some option that I am missing or how I could recover all the functionality of the plot! Thank you!

[danphillips28]

I am having the exact same issue for glimmaVolcano, eagerly awaiting a fix! Thanks, Dan

[PeteHaitch]

Can you create and provide a small example that reproduces the behaviour you're seeing? Please also provide the output of BiocManager::valid() and your RStudio version. That will really help people debug the issue.

[hasaru-k]

Howdy @joseale2310 and @danphillips28,

I've managed to reproduce the issue with the markdown options you provided.

It looks like Glimma's JS is interfering with the table of contents installation. Do the plots render if you disable the toc as below?

--- 
...
output:
  html_document:
    number_sections: yes
    theme: yeti
    # toc: yes
    # toc_float: yes
    df_print: paged
    dev: png
---

[joseale2310]

Hi, yes that seems to be the issue. I have removed the toc and the toc_float and it works fine. Weird interaction. Any chances it can be fixed? I rather prefer having the table of contents. It makes it easier for my colleagues to follow the reports I give them about their data. It would be super appreciated!

[hasaru-k]

Yes, we're looking into a fix for this interaction as a priority

[hasaru-k]

hey @joseale2310, I've pushed up a fix on a separate branch. Could you please try the following:

remove.packages("Glimma")

then:

devtools::install_github("hasaru-k/GlimmaV2@hasaru-fixTocJqueryInteraction")

And then try knitting a document with a Glimma plot. On my machine, this harmonises the interaction between the TOC installation and Glimma:

Please let me know if knitting Glimma plots with the toc + toc_float works after this.

If so, we'll endeavour to merge this fix into the main branch (after doing some further testing, as the changes involve some rearranging and updating of dependencies, which have the potential to break things).

[joseale2310]

Edit: I deleted completely the answer. I was too dumb to put any titles to any sections.

So it turns out it does seem to work very well with the fix! Thanks!!