This vignette covers common issues you may encounter when using
GiottoDB and how to resolve them.
Giotto functions do not work with GiottoDB objects
Symptom
After loading Giotto, GiottoClass,
GiottoVisuals, or the full Giotto Suite after
GiottoDB, calls such as runPCA(gobject),
normalizeGiotto(gobject),
calculateHVF(gobject), or saveGiotto(gobject)
may use the standard Giotto implementation instead of the GiottoDB
implementation.
Cause
Some Giotto functions are exported as regular functions rather than
shared generics. In R, packages loaded later appear earlier on the
search path. Loading Giotto after GiottoDB can
therefore mask GiottoDB wrappers with functions of the same name.
library(GiottoDB)
library(Giotto)
# In this load order, runPCA() resolves to Giotto::runPCA().
find("runPCA")This does not remove the GiottoDB implementation. It only changes which function is found first when an unqualified function name is used.
Solutions
Always load GiottoDB last when using unqualified
function names:
library(Giotto)
library(GiottoDB)
gobject <- normalizeGiotto(gobject)
gobject <- calculateHVF(gobject)
gobject <- runPCA(gobject)
saveGiotto(gobject, foldername = "my_giottodb_object")Alternatively, call GiottoDB functions explicitly:
gobject <- GiottoDB::normalizeGiotto(gobject)
gobject <- GiottoDB::calculateHVF(gobject)
gobject <- GiottoDB::runPCA(gobject)
GiottoDB::saveGiotto(gobject, foldername = "my_giottodb_object")This is especially important for functions with GiottoDB-specific database-backed behavior, including expression processing, PCA, saving and loading, and selected visualization methods.
A longer-term solution is planned to define more shared generics upstream in Giotto or GiottoClass, with Giotto and GiottoDB each registering methods for their supported object classes.
Why does this happen?
GiottoDB extends Giotto workflows by adding methods and wrappers for database-backed objects when needed. For functions that are not shared S3 or S4 generics in the Giotto API, R cannot dispatch to GiottoDB methods if a later-loaded package masks the GiottoDB wrapper.
How can I check which function is being called?
Use find() or inspect the function environment:
find("runPCA")
environmentName(environment(runPCA))
environmentName(environment(GiottoDB::runPCA))If the unqualified function resolves to Giotto,
GiottoClass, or GiottoVisuals, use
GiottoDB::function_name() or reload GiottoDB
last.
Getting help
If you encounter issues not covered here:
- Visit the GiottoDB issue page.
- Search for existing issues/errors that match your problem.
- If you cannot find a solution, open a new issue and include a minimal reproducible example.