run_RDR and run_BAF our of sync?

[arturspeiser]

Following the tutorial when running xclone.model.run_RDR and then xclone.model.run_BAF it fails due to a missing 'connectivities' layer in the RDR_adata file. I looked into the function and realized that the code for running KNN is not executed anymore in run_RDR.
If I instead use xclone.model.run_RDR_prev the RDR_cb_ann.obsp['connectivities'] is created and run_BAF executes without issues.

[James-Qiao]

Thank you for bringing up this issue. Indeed, KNN is not used in the current version of RDR, resulting in a bug left in the BAF module. The bug is now fixed, when running BAF, it does not require connectivities matrix from RDR. Your feedback is very much appreciated to help us improve XClone.

[arturspeiser]

Thank you for the quick answer. I implemented the changes from the PR to the xclone_baf_wrap.py file but the problem persists:

File /code/git_libs/XClone/xclone/model/smoothing.py:120, in KNN_smooth(Xdata, run_KNN, KNN_Xlayer, KNN_connect_use, layer, out_layer)
116 update_Xdata = Xdata.copy()
118 # normalize connectivities
119 # connectivities = normalize(update_Xdata.obsp[KNN_connect_use].toarray()).copy()
--> 120 connectivities = update_Xdata.obsp[KNN_connect_use].copy()
121 update_Xdata.layers[out_layer] = connectivities @ update_Xdata.layers[layer]
123 del Xdata

File /home/aspeiser/mambaforge/envs/xclone/lib/python3.9/site-packages/anndata/_core/aligned_mapping.py:213, in AlignedActual.getitem(self, key)
212 def getitem(self, key: str) -> Value:
--> 213 return self._data[key]

KeyError: 'connectivities_expr'

[James-Qiao]

Thank you again for your feedback. The variable KNN_connect_use was not updated. Now it should be fine by using the xclone_baf_wrap.py file in PR #42