# Query data formatting to map onto a reference

**URL:** <https://discourse.scverse.org/t/query-data-formatting-to-map-onto-a-reference/510>\
**Category:** scvi-tools\
**Tags:** scarches\
**Created:** [June 1, 2022, 7:20pm UTC](https://discourse.scverse.org/t/query-data-formatting-to-map-onto-a-reference/510 "2022-06-01T19:20:08Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![LuckyMD](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/luckymd/32/171_2.png) [@LuckyMD](https://discourse.scverse.org/u/LuckyMD)\
**Post date:** [June 1, 2022, 7:20pm UTC](https://discourse.scverse.org/t/query-data-formatting-to-map-onto-a-reference/510/1 "2022-06-01T19:20:08Z")

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Hey scvi-tools team!

I was wondering what the requirements are on the query AnnData object for `prepare_query_anndata()`. The documentation just says the query object should be:

> organized in the same way as data used to train model

but it’s not clear what exactly this means. Looking at the code I guess that `query_data.layers['counts']` is not supported even if the model was trained from an AnnData object that has the count data stored in a layer? I guess this might be reformatted in `setup_anndata` for the original model training? Also, does organizing both objects in the same way mean also that `query_data.var` and `query_data.obs` needs to be consistent?

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**Author:** ![Justin\_Hong](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/justin_hong/32/85_2.png) [@Justin\_Hong](https://discourse.scverse.org/u/Justin_Hong)\
**Post date:** [June 1, 2022, 7:40pm UTC](https://discourse.scverse.org/t/query-data-formatting-to-map-onto-a-reference/510/2 "2022-06-01T19:40:38Z")

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So for each kwarg used in the `setup_anndata` method for the original training data, your query data should have the corresponding data under those keys. E.g. if your count data was stored in `.layers['counts']` originally, then it should be stored there for the query data as well. The reformatting that `setup_anndata` did on the original data will be repeated on the query data. While the `query_data.var` should match, the `query_data.obs` can be different (which I assume would be the case most of the time).

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**Author:** ![LuckyMD](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/luckymd/32/171_2.png) [@LuckyMD](https://discourse.scverse.org/u/LuckyMD)\
**Post date:** [June 21, 2022, 1:08pm UTC](https://discourse.scverse.org/t/query-data-formatting-to-map-onto-a-reference/510/3 "2022-06-21T13:08:39Z")

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Thanks a lot @Justin_Hong! I think I found a bug or an incompatibility between query data prepping functions that I reported [here](https://github.com/scverse/scvi-tools/issues/1550).

Is there a way to only load the reference model schema from the model file without having to load the reference data? Then one could prep the query data depending on the model attributes. I guess this would be achievable by exposing the `_get_loaded_data()` function that is defined in `_archesmixin.py`. Otherwise I only see model load functions that require also loading the anndata object.

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**Author:** ![Justin\_Hong](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/justin_hong/32/85_2.png) [@Justin\_Hong](https://discourse.scverse.org/u/Justin_Hong)\
**Post date:** [June 22, 2022, 10:25pm UTC](https://discourse.scverse.org/t/query-data-formatting-to-map-onto-a-reference/510/4 "2022-06-22T22:25:28Z")

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Thanks for filing that issue! I’ll take a look an respond on it.

While it isn’t as extensive as the `view_anndata_setup` method, there is a static method on every model class called `view_setup_args` which tells you which kwargs were used to call `setup_anndata` on a model. This can be done without loading the data. Does this address your problem?

> **[scvi.model.SCANVI](https://docs.scvi-tools.org/en/stable/api/reference/scvi.model.SCANVI.html#view-setup-args)**
>
> Attributes table: Methods table: Attributes: adata: adata\_manager: device: history: is\_trained: test\_indices: train\_indices: validation\_indices: Methods: convert\_legacy\_save: differential\_expressio...