troutpy.pl.nmf_gene_contributions

troutpy.pl.nmf_gene_contributions#

troutpy.pl.nmf_gene_contributions(sdata, nmf_adata_key='nmf_data', save=True, vmin=0.0, vmax=0.02, saving_path='', cmap='viridis', figsize=(5, 5))#

Extracts the NMF (Non-negative Matrix Factorization) gene loadings matrix from the specified AnnData object within the spatial data (sdata), filters genes based on their maximum loading value, and plots a heatmap of the filtered loadings.

Parameters:

  • sdata (spatialdata.SpatialData) – A spatial transcriptomics dataset that contains the NMF factors in the specified key.

  • nmf_adata_key (str) – The key in sdata that contains the AnnData object with NMF results. Defaults to ‘nmf_data’.

  • save (bool) – Whether to save the heatmap plot to disk. Defaults to True.

  • vmin (float) – Minimum value for the colormap scale. Defaults to 0.0.

  • vmax (float) – Maximum value for the colormap scale. Defaults to 0.02.

  • saving_path (str) – Path where the plot should be saved if save is True. The plot is saved in a figures subdirectory.

  • cmap (str) – Colormap to use for the heatmap. Defaults to ‘viridis’.

  • figsize (tuple) – Size of the heatmap figure. Defaults to (5, 5).

Returns:

None

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