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0.5.11-notes.md

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Release Notes - cell2cell v0.5.11

New features

  • Created a new function to use external communication scores, generated with other tools. This function can be found in cell2cell.tensor.external_scores.dataframes_to_tensor().
  • Added cell2cell.tensor.tensor.BaseTensor.loc_nans, cell2cell.tensor.tensor.BaseTensor.loc_zeros, and same attributes in heirs tensor classes to keep track of values assigned with NaNs and with real zeros, respectively.
  • cell2cell.tensor.external_scores.dataframes_to_tensor() also incorporates the previous point to keep track of NaNs and real zeros when using external communication scores.
  • Added lr_fill and cell_fill parameters to cell2cell.tensor.external_scores.dataframes_to_tensor()

Feature updates

  • Added two new options to the parameter how in cell2cell.tensor.build_context_ccc_tensor(). They are: how='outer_genes' and how='outer_cells' . These new options were also extended to all InteractionTensors derived from cell2cell.tensor.tensor.BaseTensor.
  • These options of how were also extended to the new function cell2cell.tensor.external_scores.dataframes_to_tensor(), but here implemented as how='outer_lrs' and how='outer_cells'.
  • Implemented multiple to options to aggregate gene expression of protein complexes. Available options are using the minimum expression or the average expression among the subunits. This can be controlled with the parameter complex_agg_method='min' or complex_agg_method='mean' when creating a cell2cell.tensor.InteractionTensor, cell2cell.core.InteractionSpace, cell2cell.analysis.BulkInteractions pipeline, or cell2cell.analysis.SingleCellInteractions pipeline.
  • The previous point relies on the function cell2cell.preprocessing.rnaseq.add_complexes_to_expression() through the parameter agg_method='min' or agg_method='mean'
  • Added parameter cbar_label to the function cell2cell.plotting.factor_plot.loading_clustermap() to personalize the title of the color bar.
  • Added parameter manual_elbow to cell2cell.tensor.tensor.BaseTensor.elbow_rank_selection() to manually specify the elbow to highlight.

Fixed Bugs

  • Renamed cell2cell.plotting.circos_plot into cell2cell.plotting.circular_plot to avoid incompatibility with function cell2cell.plotting.circos_plot.circos_plot() that is directly imported under cell2cell.plotting