Closed cartal closed 5 years ago
Hi . Thanks for your feedback and sorry for late reply:(
We added two new parameters to batch_removal(network, adata, batch_key="batch", cell_label_key="cell_type")
. Therefore, now you can set batch_key
and cell_label_key
according to your labels in adata. Regarding the index, we added a new line to code https://github.com/theislab/scgen/blob/22dcc45c7397759e502aed818e16973fe5040180/scgen/models/util.py#L315
that should fix this issue.
Let me know if it works for you. Mo
It did! Thanks
Hi @falexwolf and @M0hammadL ,
Thanks very much for developing this tool. Is giving me amazing results!
However, right now I have an issue. The tool takes
batch
andcell_types
as main labels, then I run this as in your notebook and everything works nicely. However, whenever I try to add a new set of lables as follows:adata_hvg_scGen = adata_hvg.copy()
adata_hvg_scGen.obs["batch"] = adata_hvg.obs["source"].tolist()
adata_hvg_scGen.obs["cell_type"] = adata_hvg.obs["leiden"].tolist()
adata_hvg_scGen.obs["location"] = adata_hvg.obs["location"].tolist()
adata_hvg_scGen.obs["method"] = adata_hvg.obs["method"].tolist()
the labels are all jumbled around and they don't correspond in the UMAP. I also noticed that the index is removed from after applying
adata_corrected = scgen.batch_removal(adata_network, adata_hvg_scGen)
Do you know how to solve this?
Thanks