troutpy.tl.colocalization_proportion

troutpy.tl.colocalization_proportion#

troutpy.tl.colocalization_proportion(sdata, outpath, threshold_colocalized=1, filename='proportion_of_grouped_exRNA.parquet', save=True)#

Calculate the proportion of colocalized transcripts for each gene in the provided AnnData object.

Parameters:

  • sdata (SpatialData) – AnnData object with .X matrix containing the density of transcripts per gene.

  • outpath (str) – The directory path where the output file should be saved.

  • threshold_colocalized (int (default: 1)) – The threshold for considering a transcript colocalized (default is 1).

  • filename (str (default: 'proportion_of_grouped_exRNA.parquet')) – The name of the output file (default is ‘proportion_of_grouped_exRNA.parquet’).

Returns:

coloc DataFrame containing the proportion of colocalized transcripts for each gene.

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