pegasus.search_genes

pegasus.search_genes(data, gene_list, rec_key='de_res', measure='percentage')[source]

Extract and display gene expressions for each cluster.

This function helps to see marker expressions in clusters via the interactive python environment.

Parameters

  • data (MultimodalData or UnimodalData object) – Annotated data matrix containing the expression matrix and differential expression results.

  • gene_list (List[str]) – A list of gene symbols.

  • rec_key (str, optional, default: "de_res") – Keyword of DE analysis result stored in data.varm.

  • measure (str, optional, default: "percentage") –

    Can be either "percentage" or "mean_logExpr":

    • percentage shows the percentage of cells expressed the genes;

    • mean_logExpr shows the mean log expression.

Returns

A data frame containing marker expressions in each cluster.

Return type

pandas.DataFrame

Examples

>>> results = pg.search_genes(adata, ['CD3E', 'CD4', 'CD8'])