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Reviewer 2 comment 3 #132

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agitter opened this issue Feb 8, 2019 · 8 comments
Closed

Reviewer 2 comment 3 #132

agitter opened this issue Feb 8, 2019 · 8 comments

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@agitter
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agitter commented Feb 8, 2019

For now, the primary Manubot output is HTML intended to be viewed in a web browser. → I would insist a bit more on this part because it is a real strength if you consider a future integration with interactive figures (e.g. bokeh) and/or Jupyter notebooks. Being able to produce both a nice PDF and a HTML dynamic version would be a nice feature.

@vincerubinetti
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I'm not originally from the academic world, and I'm not familiar with Bokeh or Jupyter. Would this relate to the html front-end I'm designing? If so, any references or insight regarding these tools would be useful @agitter @dhimmel

@agitter
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agitter commented Feb 8, 2019

@vincerubinetti Bokeh is one interactive visualization library. There are others as well. Jupyter notebooks combine documentation, code, and visualization, like this example from our analysis in this particular manuscript.

I interpret this comment more generally as asking how we could support interactive manuscripts (graphics and/or code) in the HTML version of Manubot manuscripts. We touch on related work in the Concepts for the future... paragraph but don't say much. Distill, Idyll, and Stencila remain good references as we consider our response.

@agitter
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agitter commented Feb 9, 2019

Some related previous discussion manubot/rootstock#116

@slochower
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Plotly is also something to consider.

@agitter
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agitter commented Feb 12, 2019

Aside from the technical feasibility, do we have a strong vision of the desired behavior for a Manubot manuscript with interactive graphics? Specifically, would the PDF version have a static snapshot in some default initial setting in the place of the interactive graphics?

@slochower
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I don't have a strong vision, no. I think it would be something like what you say: maybe a snapshot of the first frame or some key frame. That looks like the approach taken by the remote_refocus manuscript mentioned in manubot/rootstock#116.

@dhimmel
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dhimmel commented Feb 13, 2019

would the PDF version have a static snapshot in some default initial setting in the place of the interactive graphics?

Currently, we create the PDF by rendering the HTML. Essentially, it's like we're printing the webpage to PDF. While we are likely going to switch the engine that goes from HTML to PDF as per manubot/rootstock#170, this will almost certainly remain our strategy.

Therefore, ideally interactive HTML element would convert properly to PDF. Furthermore, their default state should be the desired static view. I believe most interactive visualizations fulfill these properties.

Specifically, would the PDF version have a static snapshot in some default initial setting in the place of the interactive graphics?

Yes, exactly. Another option could be polymorphic elements where they would get replaced by a user specified static version for PDF export. For example, how the CSS @page element only affects printing. However, not sure whether this is possible? CC @vincerubinetti. And even if it is, it's probably not desirable. I don't think we really want PDF and HTML outputs diverging too much.

@agitter
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agitter commented Mar 16, 2019

Our Binder additions can be discussed in response to this.

dhimmel added a commit to dhimmel/meta-review that referenced this issue Mar 17, 2019
Interactive HTML discussion
Closes greenelab#132
dhimmel added a commit that referenced this issue Mar 20, 2019
Merges #171

Response to reviewer 2 comment 20
Closes #149

Respond to Reviewer 2 comment 3 (interactive HTML)
Closes #132
agitter pushed a commit that referenced this issue Mar 20, 2019
This build is based on
3602f67.

This commit was created by the following Travis CI build and job:
https://travis-ci.org/greenelab/meta-review/builds/509153211
https://travis-ci.org/greenelab/meta-review/jobs/509153212

[ci skip]

The full commit message that triggered this build is copied below:

Address review 2-3 & 2-20: dot plot & interactive HTML

Merges #171

Response to reviewer 2 comment 20
Closes #149

Respond to Reviewer 2 comment 3 (interactive HTML)
Closes #132
agitter pushed a commit that referenced this issue Mar 20, 2019
This build is based on
3602f67.

This commit was created by the following Travis CI build and job:
https://travis-ci.org/greenelab/meta-review/builds/509153211
https://travis-ci.org/greenelab/meta-review/jobs/509153212

[ci skip]

The full commit message that triggered this build is copied below:

Address review 2-3 & 2-20: dot plot & interactive HTML

Merges #171

Response to reviewer 2 comment 20
Closes #149

Respond to Reviewer 2 comment 3 (interactive HTML)
Closes #132
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