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
orUnimodalData
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 indata.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.
- Can be either
- Returns
A data frame containing marker expressions in each cluster.
- Return type
pandas.DataFrame
Examples
>>> results = pg.search_genes(adata, ['CD3E', 'CD4', 'CD8'])