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

Question

Programatically my bookdown project proceeds as follows:
Reading in raw data - produces all kind of stats.
Data preprocessing (logarithmization, normalization, imputation) - produces various plots for monitoring the population-level defects incurred.
PCA for analysis QC - produces plots for PCA and loadings-dominating data points.
Differential expression analysis - produces volcano plots and plots characterizing prominent differentially expressed features.
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.

Answer 1

You could do the following:
Split steps 1-3 and 4-5 into two speparate *.Rmd files, say 123.Rmd and 45.Rmd.
Add a code chunk to the beginning of 45.md that knits 123.Rmd to 123.md:
```{r knit123, include = FALSE}
knitr::knit("123.Rmd", output = "123.md")
```
This will generate the output of steps 1-3 in Markdown and make all the objects created thereby available to steps 4-5.
Add a code chunk to the end of 45.Rmd that reads 123.md prints its content:
```{r include123, results = "asis"}
cat(readLines("123.md"), sep = "\n")
```
The results = "asis" will prevent any further processing as it is already valid Markdown.
Knit 45.Rmd to whatever target format you want.
edit (1):
TL;DR: Instead of storing the object from steps 1-3 in memory throughout steps 4-5 in order to print them afterwards, print them first and store the results on disk.
edit (2):
Since you explicitely mentioned bookdown: I would not be surprised if there was a YAML option to include a Markdown file at the end of the knitting process (something like include-after: 123.md); but I don't know for sure from the top of my head and I'm too lazy to look it up myself. ;-)