bookdown/rmarkdown/knitr: Non-code sequential processing howto?

[r-cheologist]

This comes from an earlier post to stackoverflow ...

Programatically my bookdown project proceeds as follows:

1. Reading in raw data - produces all kind of stats.
2. Data preprocessing (logarithmization, normalization, imputation) - produces various plots for monitoring the population-level defects incurred.
3. PCA for analysis QC - produces plots for PCA and loadings-dominating data points.
4. Differential expression analysis - produces volcano plots and plots characterizing prominent differentially expressed features.
5. Overrepresentation analysis of the differentially expressed features from 4. in various biological ontology systems - produces example bar plots for enriched categories.

I have analysis and narrative nicely integrated using bookdown, enabling efficient on fly discarding of temporary (sizable) data sets/ggplot2 objects (pre/post transformation data etc.).

HOWEVER: The target audience is mostly/only interested in 4. & 5., leading me to the aspired to following structure:

4., 5., Appendix(1., 2., 3.)

Is there any other way but precomputing 1.-5. and then revisiting in the targeted order - I would prefer to avoid accumulating all those ggplot2 objects in memory if at all possible.

[mschilli87]

@r-cheologist: I tried to answer your SO question. I hope it helps. If so, please close this issue.

PS: I wanted to point out that I saw your SO question before seeing this github issue (I follow bookdown on both platforms, but on SO there are likely more followers). So also without this issue you would have gotten my attention and answer. I'd suggest to at least wait for a couple of days before cross-posting (if at all), as not everyone has time every day or is even close to your time zone. 😉

[r-cheologist]

Thank you! A indicated on stackoverflow, I am actively using your proposal and thus close this.

[github-actions]

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