Modify AnnDataSets obs matrix

[nvelthuijs]

Hi,
I've been trying to work with a 20-sample scATAC library, but keep having issues with accessing the .obs-matrix.

What is the intended way of adding columns to or manipulating values in the .obs?

For example, say I want to take the fragment counts from the original adata_objects data.adatas.obs["n_fragment"] and write their log10 to data.obs["n_fragment_log10"]?

I can get the values:

np.log10(data.adatas.obs["n_fragment"])

Shape: (62223,)
--
f64
4.374987
3.326541
4.028449
3.351603

But how do you write that to data.obs?
data.obs["n_fragment_log10"] = np.log10(data.adatas.obs["n_fragment"])
AttributeError: 'DataFrame' object has no attribute 'with_column'

data.obs = data.obs[:].with_columns(np.log10(data.adatas.obs["n_fragment"].alias("n_fragment_log10")))
PanicException: called `Result::unwrap()` on an `Err` value: H5Ldelete(): no name

data.obs[:] = data.obs[:].with_columns(np.log10(data.adatas.obs["n_fragment"].alias("n_fragment_log10")))
ValueError: Cannot __setitem__ on DataFrame with key: 'slice(None, None, None)' of type: '<class 'slice'>' and value: 'shape: (62_223, 3)

Thanks in advance,
Niels

[kaizhang]

The code below is working for me:

data.obs['n_fragment'] = np.log10(data.adatas.obs["n_fragment"])

which version are you using?

[nvelthuijs]

I'm using version 2.2.0.
Polars version 0.17.2.

[kaizhang]

I'm going to release v2.3 in a few hours and this should fix the problem. v2.3 is a highly recommended upgrade as it comes with tremendous improvements. But you will have to rerun everything using the new version. Please read the ChangeLog: https://github.com/kaizhang/SnapATAC2/blob/main/ChangeLog.md