comparison decoupler_pseudobulk.py @ 11:70a5c6f2408d draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit f6c6b8e014c99101232dc75aa972a12fc640a4de

10:f6040492b499

        # of the contrast to have the genes expressed above
        # the threshold of % of cells to be of interest.
        for condition in conditions:
            # remove any starting or trailing whitespaces from condition
            condition = condition.strip()
            # check the percentage of cells that express each gene
            # Filter the AnnData object based on the obs_field value
            adata_filtered = adata[adata.obs[obs_field] == condition]
            # Calculate the percentage of cells expressing each gene
            gene_expression = (adata_filtered.X > 0).mean(axis=0) * 100

11:70a5c6f2408d

        # of the contrast to have the genes expressed above
        # the threshold of % of cells to be of interest.
        for condition in conditions:
            # remove any starting or trailing whitespaces from condition
            condition = condition.strip()
            if condition not in adata.obs[obs_field].unique():
                raise ValueError(
                    f"Condition '{condition}' from contrast {contrast}"
                    f" is not present in the "
                    f"obs_field '{obs_field}' from the AnnData object."
                    f"Possible values are: "
                    f"{', '.join(adata.obs[obs_field].unique())}."
                )
            # check the percentage of cells that express each gene
            # Filter the AnnData object based on the obs_field value
            adata_filtered = adata[adata.obs[obs_field] == condition]
            # Calculate the percentage of cells expressing each gene
            gene_expression = (adata_filtered.X > 0).mean(axis=0) * 100