Comments (3)
@PedroMilanezAlmeida I just pushed a change to the master branch so the development version of uwot will now return the fuzzy graph used for transforming if you pass ret_extra = c("fgraph")
, e.g.:
iris_train <- iris[1:100, ]
iris_test <- iris[101:150, ]
iris_train_umap <- umap(iris_train, ret_model = TRUE)
iris_test_umap <- umap_transform(iris_test, iris_train_umap, ret_extra = c("fgraph"))
iris_test_umap$embedding # the coordinates
iris_test_umap$fgraph # the fuzzy graph
the returned fuzzy graph has as many rows as there are items in the new data to transform, and as many columns as there were items in the data used to build the model, so in the example above dim(iris_test_umap$fgraph) == c(50, 100)
.
This will eventually appear in the next CRAN release (which is unlikely to be submitted before the end of the year).
from uwot.
It does internally create the fuzzy graph but it doesn't output it, sorry.
It should be possible to add this functionality without too much difficulty though.
from uwot.
Thank you very much for your quick reply and solution. I appreciate it! I'll close this for now and, in the unlikely event of running into any issues, I'll let you know. Thanks again!
from uwot.
Related Issues (20)
- Test failure an arm64, ppc64el and s390x HOT 8
- Add general_simplicial_set_intersection to the uwot API HOT 3
- umap_transform causes R Studio to abort (R encountered a fatal error.) HOT 4
- umap_transform can give odd results with dens_scale HOT 17
- Citing {uwot} HOT 1
- Weird looking UMAP for spectral flow data HOT 3
- What C++ version should CXX_STD have? HOT 16
- devtools can no longer build uwot on Windows HOT 5
- I can not load the saved model, an example from the help HOT 9
- Reproducibility issue with the same data and OS HOT 17
- umap_transform with seurat umap coordinate HOT 2
- dgCMatrix_colSums' not found error when using a binary matrix HOT 2
- irlba as_cholmod_sparse problems HOT 1
- maybe unintended data use in examples HOT 2
- umap_transform uses a different distance metric if loaded in HOT 5
- `fuzzy_simplicial_set()` for BBKNN HOT 5
- Differences in model parameters when calling umap() causes umap_transform() to error HOT 3
- How to input similarity_graph back into umap parameters? HOT 3
- Range scale input before optimization HOT 2
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from uwot.