``` {r, echo = FALSE} knitr::opts_chunk$set(eval = FALSE)
This vignette should serve as a supplement to the Get Started vignette (`vignette("scdrake")`) and expects you have finished the initial three steps. Other "hot" topics and questions can be found in `vignette("scdrake_faq)` *** ## Retrieving intermediate results (targets) In `{drake}`'s terminology, a pipeline is called *plan*, and is composed of *targets*. When a target is finished, its value (object) is saved to cache (the directory `.drake` by default). The cache has two main purposes: - If a target is not changed, its value is loaded from the cache. *Change* involves e.g. target's definition (code) or change in upstream targets on which the target depends. This way `{drake}` is able to skip computation of finished targets and greatly enhance the runtime. More details [here](https://books.ropensci.org/drake/triggers.html). - Users also have access to the cache, and so you can load any finished target into your R session. Users can access the cache via two `{drake}`'s functions: - `drake::loadd()` loads target's value to the current session as a variable of the same name. - `drake::readd()` returns target's value (so it can be assigned to variable). Let's try it and load the filtered `SingleCellExperiment` object: ```r drake::loadd(sce_final_input_qc)
Value of the target sce_final_input_qc
was loaded as a variable of the same name to your current R session
(or more precisely, to the global environment).
Similarly, we can load this target to a variable of our choice:
sce <- drake::readd(sce_final_input_qc)
And work further with the loaded object, e.g.
scater::plotExpression(sce, "NOC2L", exprs_values = "counts", swap_rownames = "SYMBOL")
scdrake
plans?For a more schematic overview of pipelines and stages see vignette("pipeline_overview")
, where are also
diagrams.
Advanced users might be interested in looking into source code of {scdrake}
's plans
(files named plans_*.R
).
qs
)By default, R's Rds
format is used (see ?saveRds
) to save intermediate results to {drake}
s cache,
but instead, we recommend to use DRAKE_FORMAT: "qs"
(see https://github.com/traversc/qs) in config/pipeline.yaml
that offers better performance, but sometimes doesn't work correctly (drake
throws untraceable errors).
See https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets for more details.
See vignette("scdrake_extend")
, please.
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