Wrapper function to conduct the full regulatory topic-modeling workflow for one selected topic-document construction method.
Usage
run_topic_modeling(
filtered_dir,
multiomic_data = NULL,
comparisons,
output_dir,
project_config = NULL,
method = NULL,
k_grid = NULL,
warplda_iterations = NULL,
topic_link_output = NULL,
vae_device = NULL,
vae_batch_size = NULL,
pathway_backend = NULL,
...
)Arguments
- filtered_dir
Directory containing Module 3 filtered differential-link files.
- multiomic_data
Optional CraftGRN multiomic object. Required when `replicate_documents = TRUE`.
- comparisons
Comparison or condition grouping table, or a CSV path.
- output_dir
Topic output directory.
- project_config
Optional project YAML path or config list. When supplied, `topic_method`, `topic_k` or `topic_k_grid`, `warplda_iterations`, and `topic_link_output` are used for arguments that are left as `NULL`.
- method
Single Module 3 method ID. If `NULL`, read from `project_config` or use the package default.
- k_grid
Integer topic numbers. If `NULL`, read from `project_config` or use `10`.
- warplda_iterations
Number of native WarpLDA iterations. If `NULL`, read from `project_config` or use `2000`.
- topic_link_output
Topic-link output mode. If `NULL`, read from `project_config` or use `"pass"`.
- vae_device
VAE device, for example `"auto"`, `"cpu"`, or `"cuda"`. If `NULL`, read from `project_config` or use `"auto"`.
- vae_batch_size
VAE mini-batch size. If `NULL`, read from `project_config` or use `64`.
- pathway_backend
Pathway enrichment backend. Use `"enrichly"` for local cached enrichment or `"enrichr"` for the Enrichr web API. If `NULL`, read from `project_config` or use `"enrichly"`.
- ...
Additional arguments passed to the internal topic-modeling wrapper.