Normalizations, Feature Selections, DimReduction S3 class, (Iterative) Lsi Implementation, Partial function framework, Clustering changes and Framework#189
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immanuelazn wants to merge 149 commits intobnprks:mainfrom
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…`save_lsi`, remove `save_in_memory` in `lsi()`
rewrite `convert_mat_to_cluster_matrix()` to always convert to graph adjacency matrix. rename `convert_mat_to_cluster_matrix()` to `convert_mat_to_graph()`. Add input checking for knn to graph functions
immanuelazn
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Mar 3, 2025
| #' @param n_iterations (int) The number of LSI iterations to perform. | ||
| #' @param feature_selection_method (function) Method to use for selecting features for LSI. | ||
| #' Current builtin options are `select_features_variance`, `select_features_dispersion`, `select_features_mean`, `select_features_binned_dispersion` | ||
| #' @param cluster_method (function) Method to use for clustering the post-SVD matrix. |
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Not too happy explicitly describing usage of partial functions here. Perhaps we can replace this once the test data is in, and we can show the small vignette with norms, feature selection, clustering + LSI. On top of that, we can just show usage directly with examples.
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integrate `cluster_cells_graph()` into codebase
…k on IterativeLSI
export `cluster_cells_graph()`
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Meta-PR that describes the culmination of efforts of multiple features.
Included and previously described features: