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The previous `sc.pl.umap` etc. had an option to export legend positions via 'on data export'. We need a solution in the docs... Presumably just by exposing the cached positions to the user.
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I'm trying to compile CLV on my Mac. I get to step 6, typing 'make' in the TreeScaper folder and then I get errors.
The pre-compiled CLV for Mac works great, so I've been using that. I wanted to l…
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Hi, great program.
I am running cytofkit with pretty conventional parameters on a large set of samples. Some files have very few cells; several hundred. Most have a large number of cells.
I am g…
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Hi,
I am having an issue exporting my h5ad file to spring for visualization. I have been following the [spring export tutorial](https://github.com/theislab/scanpy_usage/tree/master/171111_SPRING_ex…
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I'm following the installation instructions from the Manual v1 (released 4/4/2917) 3 Installation, "Command-line versions of TreeScaper can be generated by following these instructions" (Step (1), (2)…
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Hi,
I am trying to import a dataset from 10X Visium H&E
I am importing the dataset with:
```python
adata = sq.read.visium('path')
adata.var_names_make_unique()
```
Then pre-processing:
```py…
Lem-P updated
3 months ago
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When I use `sc.pp.log1p(adata)` and then `sc.pp.log1p(adata, layer='other')` it warns me that the data has already been logged even though I am logging a layer as opposed to adata.X.
Would be nic…
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**Update** Note sure if it is a problem with our script. However, if colors are not found, can it use default color-map and let us plot after raising a warning?
Log is following. ~Working on a PR.…