scanpy
scanpy copied to clipboard
scverse
Single-cell analysis in Python. Scales to >1M cells.
When doing so, adata cannot be saved as a file in the h5ad format.
In the [heatmap docs](https://scanpy.readthedocs.io/en/stable/generated/scanpy.pl.heatmap.html): > save : [Union](https://docs.python.org/3/library/typing.html#typing.Union)[[str](https://docs.python.org/3/library/stdtypes.html#str), [bool](https://docs.python.org/3/library/functions.html#bool), [None](https://docs.python.org/3/library/constants.html#None)] (default: None) > ... A string is appended to the default filename Unlike matplotlib, scanpy forces the user to adopt...
Currently there's only a wrapper for `scanorama.integrate_scanpy` From https://github.com/brianhie/scanorama: > The function integrate_scanpy() will simply add an entry into adata.obsm called 'X_scanorama' for each adata in adatas. obsm['X_scanorama'] contains the...
From the [scanpy docs](https://scanpy.readthedocs.io/en/stable/generated/scanpy.pl.umap.html): > legend_loc : [str](https://docs.python.org/3/library/stdtypes.html#str) (default: 'right margin') >> Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter of [Legend](https://matplotlib.org/stable/api/legend_api.html#matplotlib.legend.Legend)....
- [x] Additional function parameters / changed functionality / changed defaults? - [ ] New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`?...
- [x] I have checked that this issue has not already been reported. - [x] I have confirmed this bug exists on the latest version of scanpy. - [ ]...
- [x] I have checked that this issue has not already been reported. - [x] I have confirmed this bug exists on the latest version of scanpy. - [ ]...
The allen institute has published a nomenclature for brain cell types with 127 types. When I annotate my cells with those types, the umap plot doesn't color the cells: Would...
According to [scanorama MemoryError](https://github.com/brianhie/scanorama/blob/master/scanorama/scanorama.py#L768-L775), I think `batch_size` parameter doesn't work for `sc.external.pp.scanorama_integrate` ### Minimal code sample (that we can copy&paste without having any data) ```python sc.external.pp.scanorama_integrate(adata, key="datasetID", batch_size=500) ``` ```pytb...
