Sten Linnarsson

Infinite Euclidean distances when random seed is unlucky number 13

4

When the numpy random seed is set to [unlucky number 13](https://en.wikipedia.org/wiki/Triskaidekaphobia), this code snippet: ```python from pynndescent import NNDescent X = np.load("X.npy") np.random.seed(13) nn = NNDescent(data=X, metric="euclidean", n_jobs=-1) di, d...

Hi - thanks for developing pyMDE! I am trying to create an embedding like tSNE or UMAP, but with additional bias on the embedded space. For example, I have single-cell...

[FEATURE REQUEST] Plot zeros in grey, nonzero using colormap

1

The difference between zero (no detection) and nonzero values is dramatic and informative in single-cell analysis. This is especially true when some clusters are all-zero whereas some other clusters have...

Single-cell data is sparse (i.e. there are many zeros), and the difference between not-expressed (zero) and expressed (1, 2, 3, ...) can be highly informative. Currently cellxgene plots data using...

Create useful documentation for margins

1

I would like to increase the font size for the axis tick marks. Maybe I'm not doing it right (but I also could not find any documentation for how it...