Francesca Drummer

Sliding window across spatial neighbourhood

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## Description Implementation of sliding window (inspired by [Kasumi](https://www.biorxiv.org/content/10.1101/2024.03.06.583691v1)) over a spatial neighbourhood or view. Input: - window size - overlap Output: - assignment of cells to sliding window

Sliding window

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## Description This PR adds a new function, sliding_window, to the codebase. The sliding_window function divides a tissue slice into regularly shaped, spatially contiguous regions (windows). It allows for the...

### Description of feature When initialised the GraphAnnDataModule there is a graph_loader and spatial_node_loader. Currently, they load the entire dataset as batches. For self-supervised learning strategies it is necessary to...

GraphAnnDataModule with custom split

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### Description of feature Currently the GraphAnnDataModule randomly splits the PyG Data object according to a pre-defined train, val and test size. It would be good to allow the user...

### Report ``` /ictstr01/home/icb/francesca.drummer/1-Projects/geome/src/geome/transforms/categorize.py:38: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual. getattr(adata, self.axis)[key] = getattr(adata, self.axis)[key].astype("category") ``` ### Version information _No response_

missing var_names in BasePlot

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- [x] Closes #3387 - [ ] Tests included or not required because: - [ ] Release notes not necessary because:

"Interactive" Dotplot version: check for available var_names

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### What kind of feature would you like to request? Additional function parameters / changed functionality / changed defaults? ### Please describe your wishes ## Feature Change dotplot to a...

### Report #62 merged without tests for `test/test_one_hot_encode.py`. Write tests for `one_hot_encode` feature ### Version information _No response_