Comments (7)
update:
The 'dtype' is missing in _read_text()
return AnnData(data,
obs={'obs_names': row_names},
var={'var_names': col_names})
Similarly, in transpose()
and copy()
,etc, it's missing too
from anndata.
It should be present in _read_text
, right and the other reading function! That's a bug. Would you mind making a pull request?
It shouldn't be present in transpose
and copy
, though.
from anndata.
Sure. I will do that.
But I noticed for the function transpose() , if I donβt add dtype = float64, after read_text() and transpose, it will be reverted to float32 again . I guess there must be something else that needs to be fixed.
from anndata.
Hi Alex,
Thanks again for developing this amazing package for python community. I was wondering if you have any updates on the data type issue. I'll be happy to pull request if you could let me know besides reading functions all the other functions I should look at.
Many thanks!
Best,
Huidong
from anndata.
Sorry for being so slow, @huidongchen , it's been fixed for copy (989f13e) and for transpose (b7dca41).
The PR for the read functions will only affect the read functions themselves. Should be very straight forward. Thank you!
from anndata.
Hi Alex @falexwolf thanks a lot for updating other relevant parts. I will make a PR shortly.
from anndata.
Fixed via #81.
from anndata.
Related Issues (20)
- Add working `GroupStorageType` type annotation
- 0.10.6 - Cannot write files due to implicit conversion to str dtype. HOT 2
- Saving .h5ad with pd.Series in .uns results in IORegistryError HOT 3
- `read_elem_as_dask` HOT 8
- `FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'` on CI HOT 2
- Upcoming Scipy 1.13 incompatible with file-backed sparse matrices
- CZI files' `var` count changd
- `/` in column names makes AnnData Zarr object unreadable on windows HOT 12
- String indexes in var lead to UserWarning HOT 1
- Move tests out of the package
- Refactor `BaseCompressedSparseDataset` and subclasses to remove `backed_{csr,csc}_matrix`
- concat_on_disk should use int64 indptrs by default so that it can concatenate large files HOT 4
- TypeError: Can't implicitly convert non-string objects to strings HOT 4
- Error concatenating scRNA with visium dataset
- Error: Expected a python object, received a character HOT 1
- memory usage of concat HOT 3
- Using `Pint` for units HOT 9
- UMAP of gene subset of adata HOT 2
- Error using sc.pl.stacked_violin HOT 1
- NotImplementedError with concat_on_disk
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
π Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. πππ
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google β€οΈ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from anndata.