Cell2cell

Please refer to the release notes of all previous versions [here](https://github.com/earmingol/cell2cell/tree/master/release)

New features
- Refer to [v0.7.2 notes](./0.7.2-notes.md) to see the previous new features.
- Added example of using Spatial Data with Tensor-cell2cell.

Feature updates
- Updated single-cell data example with cell2cell to use COVID-19 data.
- Updated bulk data example with cell2cell.
- Updated `docs` folder for readthedocs.org.
- Updated README.md

Fixed Bugs
- Fixed legend visualization in `cell2cell.plotting.pcoa_plot.pcoa_3dplot()`
- Fixed negative P-values in `cell2cell.stats.permutation.compute_pvalue_from_dist()`
- Fixed permutation analysis in `cell2cell.analysis.cell2cell_pipelines.SingleCellInteractions`
- Fixed legend visualization in `cell2cell.plotting.circular_plot.circos_plot()`

Please refer to the release notes of all previous versions [here](https://github.com/earmingol/cell2cell/tree/master/release)

New features
- Added `cell2cell.spatial` functions for enabling analyses considering spatial organization in spatial data.
These functions include:
- Filtering by intercellular distances by thresholding values (`cell2cell.spatial.distances` and `cell2cell.spatial.filtering`).
- Dividing the tissue in square grids (`cell2cell.spatial.neighborhoods.create_spatial_grid()`)
- Dividing the tissue in moving windows (`cell2cell.spatial.neighborhoods.create_sliding_windows()`, `cell2cell.spatial.neighborhoods.calculate_window_size()`,
and `cell2cell.spatial.neighborhoods.add_sliding_window_info_to_adata()`)

Feature updates


Fixed Bugs
- Fixed bug that made to incorrectly visualize multiple legends in plots as for example in `cell2cell.plotting.tensor_plot`
when using newer matplotlib versions.

Please refer to the release notes of all previous versions [here](https://github.com/earmingol/cell2cell/tree/master/release)

Fixed Bugs
- Fixed bug that was skipping first factor to generate outputs from `cell2cell.external.gseapy.run_gsea()`

New features
- Direct access to `interaction_elements` attribute from `cell2cell.analysis.cell2cell_pipelines.SingleCellInteractions`
and `cell2cell.analysis.cell2cell_pipelines.BulkInteractions`
- Added option to store GMT file in output_folder in `cell2cell.external.gseapy`

Feature updates
- Removed tqdm for jupyter notebooks.
- Updated tensorly version from 0.7.0 to 0.8.1

Fixed Bugs
- Modified permutations in `cell2cell.analysis.cell2cell_pipelines.SingleCellInteractions.permute_cell_labels()`

New features
- Added new attributes and methods to `cell2cell.tensor.tensor.BaseTensor` and any other
derived class, including `BaseTensor.shape`, `BaseTensor.write_file()`, `BaseTensor.to_device()`.
These new features are respectively for:
- Passing the shape of the tensor directly (instead of `BaseTensor.tensor.shape`)
- Export or save a tensor object to a file.
- Change the device for running Tensor-cell2cell (e.g. 'cpu', 'cuda', etc.)
-
Feature updates
- Added **kwargs as parameter of `cell2cell.analysis.tensor_pipelines.run_tensor_cell2cell_pipeline()`
to directly pass parameters to the functions running the elbow analysis and the tensor decomposition.
- Sort factors numerically in `cell2cell.external.gseapy.run_gsea()`.

Fixed Bugs
-

New features
- Implemented in-house GSEA using gseapy. Associated code is located in
`cell2cell.datasets.gsea_data` and `cell2cell.external.gseapy`.
- Implemented a function to obtain a dataframe of lr pairs by cell pairs from a tensor decomposition
result, so it can be use to make a plot. It can compute a communication score that is by factor or
across all factors. See function `cell2cell.analysis.tensor_downstream.get_lr_by_cell_pairs()`.

Feature updates
- Added the axis names to the dataframe generated with cell2cell.analysis.tensor_downstream.get_joint_loadings(),
which correspond to the `dim1` and `dim2` parameters.
- Added the axis labels (`cm.ax_heatmap.set_xlabel()` & (`cm.ax_heatmap.set_ylabel()`) using the dataframe axis names
passed to cell2cell.plotting.factor_plot.loading_clustermap()

What's Changed
* Minor update to examples & docs by earmingol in https://github.com/earmingol/cell2cell/pull/23
* Updates for v0.6.5 by earmingol in https://github.com/earmingol/cell2cell/pull/24


**Full Changelog**: https://github.com/earmingol/cell2cell/compare/v0.6.4...v0.6.5