James Melville

My initial experiments with connectivity plotting have confirmed my suspicions that without access to something that works like [datashader](https://datashader.org/) (which the Python connectivity plotter makes use of), the naïve approach...

https://schochastics.github.io/edgebundle/ seems worth exploring

Think this got fixed

Unfortunately, I cannot give you a satisfactory solution to these issues. As far as I can tell, we are at the mercy of whatever system libraries are part of the...

One thing that could cause issues is the `spca` initialization: here you are the mercy of the SVD routine which also can produce arbitrary signs, e.g. from the man page...

Although not as convenient as full integration with uwot, [rnndescent](https://cran.r-project.org/package=rnndescent) supports the Jaccard/Tanimoto coefficient with binary data. See [the rnndescent article](https://jlmelville.github.io/uwot/articles/rnndescent-umap.html) for details on using it with uwot.

Closing this for now, because future-me is still not inclined to implement densMAP any more than past-me was.

Unfortunately, I don't know anything about seurat, so I don't know what the `seurat@reductions$umap` object is. Is it the output coordinates of running UMAP on your RNA data (presumably a...

Closing as not reproducible. Please reopen if there is more info and this is not an issue better dealt with at the Seurat repo.

Hello, so it seems that there is evidence from multiple users that running: ```R library(recipes) library(embed) rec % step_umap(all_numeric_predictors(), num_comp = 2) embed:::prep.step_umap(rec$steps[[1]], iris, rec$var_info) #> UMAP embedding for Sepal.Length,...