initialize_app_env.RdPopulate the app environment
initialize_app_env(app_env, cells, counts, pc_space, embedding, nn, k)
| app_env | R environment, app enviroment |
|---|---|
| cells | data.frame, containing cell metadata |
| counts | sparse matrix, containing counts (cols = cells, genes = rows) |
| pc_space | matrix, containing PCA coordinates (cols = coordiantes, rows = cells) |
| embedding | matrix, containing coordinates for two-dimensional embedding (cols = coordiantes, rows = cells) |
| nn | list, containing nearest neighbor information (created by run_nn function) |
| k | numeric, number of neighbors considered for smoothing (default k = 50) |