Reformat output report as HTML following WG consensus #3
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Makefile runs the 3 main scripts/steps of analysis on those test files.
Add rmd2html.R driver as a first step. This won't work because it doesn't pass the CLI options through to Rmd.
It's missing a couple of subsection titles, but the plots and tables are all there and identical to the PDF report.
- Save external images locally - Add latex dependencies to Dockerfile Not on by default, yet, pending: - config change (and rename) in rmd2html.R - table wrap/clipping issue in the output PDF
Those additional plots and table were not useful to users.
mcrocker-bioborg
approved these changes
Dec 14, 2023
- Remove commented lines from conda config - Ensure r-markdown is in both the main and dev conda environments. - test/Makefile: target HTML as the "fast" outputs to build and remove
Fix Rmd formatting (with minimal content changes) to make the LaTeX->PDF rendering look good.
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This PR adds a new script,
create_report.R, and parameterized Rmarkdown document,report.Rmd, to generate an HTML (or potentially PDF) report functionally equivalent to the original PDF, but updated according to the AAV working group consensus so far.Tangential updates:
test/Makefileto generate the new HTML reports, and fix some quirks.