activate_python | R Documentation |
This function activates a Python environment (default: "seuratextend") and imports specified packages. It's particularly important for macOS users to call this function at the beginning of their workflow to prevent R session crashes when running Python-dependent functions later.
activate_python(conda_env = "seuratextend", verbose = TRUE, packages = c("os"))
conda_env |
Character string specifying the conda environment name. Default is "seuratextend". |
verbose |
Logical indicating whether to print status messages. Default is TRUE. |
packages |
Character vector of Python packages to import. |
This function serves two main purposes:
1. It activates the specified conda environment and imports the specified Python packages.
2. **For macOS users (especially on Apple Silicon M1/M2/M3/M4)**: Running this function at the start of your R session, before loading any R objects, prevents memory management issues between R and Python that can otherwise cause R to crash when running operations like PCA on AnnData objects.
This is a crucial first step for macOS users working with 'scVelo' functions.
Invisible TRUE if successful
## Not run:
# For macOS users, run this at the beginning of your session
activate_python()
# Then load your Seurat objects and continue with your analysis
seu <- readRDS("my_seurat_object.rds")
# Custom environment with verbose output
activate_python(conda_env = "my_custom_env", verbose = TRUE)
## End(Not run)
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