v0.7.4

Please refer to the release notes of all previous versions here

New features

• Refer to v0.7.3 notes to see the previous new features.

Feature updates

• Updated assert warnings for Tensor-cell2cell

Fixed Bugs

• Fixed set indexing that was deprecated in new pandas versions (in cell2cell.preprocessing.rnaseq.add_complexes_to_expression())

What's Changed

• Updated Spatial Example by @earmingol in #47

Full Changelog: v0.7.3...v0.7.4

cell2cell - v0.7.3

Please refer to the release notes of all previous versions here

New features

• Refer to v0.7.2 notes 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()

cell2cell - v0.7.0 and v0.7.1

Please refer to the release notes of all previous versions here

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.

cell2cell - v0.6.8

Please refer to the release notes of all previous versions here

Fixed Bugs

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

cell2cell - v0.6.7

Please refer to the release notes of all previous versions here

Release Notes - cell2cell v0.6.7

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()

cell2cell - v0.6.6

Please refer to the release notes of all previous versions here

Release Notes - cell2cell v0.6.6

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

cell2cell - v0.6.5

Please refer to the release notes of all previous versions here

Release Notes - cell2cell v0.6.5

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 #23
• Updates for v0.6.5 by @earmingol in #24

Full Changelog: v0.6.4...v0.6.5

cell2cell - v0.6.4

Please refer to the release notes here.

Release Notes - cell2cell v0.6.4

New features

• Added a the cell2cell.io.read_data.load_tensor() function to directly load a previously
  exported interaction_tensor variable generated with Tensor-cell2cell.
• Added a new dataset from a COVID-19 study. Available in cell2cell.datasets.anndata.balf_covid().
• Added functions to create and explore directories in cell2cell.io.directories.
• Added cell2cell.io.read_data.load_tables_from_directory() to load all tables or dataframes with the same
  extension that are located in such directory.

Feature updates

• Modified sparsity_fraction() and missing_fraction() methods of cell2cell.tensor.tensor.BaseTensor to return
  the item in the tensorly tensor object.
• Added progress bar to cell2cell.tensor.external_scores.dataframes_to_tensor().
• Added the option to specify the backend when running cell2cell.analysis.tensor_pipelines.run_tensor_cell2cell_pipeline().

Fixed Bugs

• Implemented a way to manage duplicated instances of a LR comm score in cell2cell.tensor.external_scores.dataframes_to_tensor().
  It can be controled through the parameter dup_aggregation.

What's Changed

• Code restructuring by @earmingol in #3
• Added core pipeline by @earmingol in #4
• Code reorganization by @earmingol in #5
• v0.5.10 by @earmingol in #8
• New version - v0.5.11 by @earmingol in #11
• Updates for v0.6.0 by @earmingol in #12
• Updates for v0.6.1 by @earmingol in #15
• Updates for v0.6.2 by @earmingol in #17
• Updates for v0.6.3 by @earmingol in #18
• Quick rebase by @earmingol in #20
• Updates for v0.6.4 by @earmingol in #21

New Contributors

• @earmingol made their first contribution in #3

Full Changelog: https://github.com/earmingol/cell2cell/commits/v0.6.4