aopisco

hi all, I have a plotly sankey diagram that I'd like to add to my react app. I followed the tutorial but can't get the Sankey plot to show. do...

use only highly variable genes -- de.test.lrt and de.test.wald not working otherwise

4

I have an anndata object which I did not subset to the highly variable genes - if I use that as the input neither lrt or wald can converge. I'm...

de.test.pairwise very slow

5

@davidsebfischer do you have any plans for speeding up pairwise test? currently I'm trying with an AnnData object with n_obs × n_vars = 1740 × 5829 but it is taking...

how close from a cluster is something unassigned?

2

is there a way to know the clusters that a cell classified as unassigned is closest to? is there a way to output a confusion matrix?

getSankey function

1

The current version of the output is very limited regarding customization. Are there any plans on upgrading that to use more flexible libraries, such as Plotly? https://plot.ly/r/sankey-diagram/

issue with `_validate_lengths`: needed to downgrade to `numpy 1.15`

1

When doing from numpy.lib.arraypad import _validate_lengths I'm getting the following error: ``` --------------------------------------------------------------------------- ImportError Traceback (most recent call last) in ----> 1 from numpy.lib.arraypad import _validate_lengths ImportError: cannot import name...

exporting data

3

It would be incredibly useful to be able to export the figures as pngs or vectorial figures. I've shared our dataset with collaborators and they are either taking screenshots or...

@mbrbic can you take a look at https://github.com/singlecellopenproblems/SingleCellOpenProblems/issues/115