ovrlpy.get_pseudocell_locations
- ovrlpy.get_pseudocell_locations(df, genes=None, min_distance=10, KDE_bandwidth=1, min_expression=5)
Returns a list of local maxima in a kde of the data frame, interpreted as locations with high likelyhood to contain a cell.
- Parameters:
df (DataFrame) – A dataframe of coordinates.
genes (list, optional) – A list of genes to include in the expression model. Defaults to all genes in the dataframe.
min_distance (int, optional) – The minimum distance between local maxima.
KDE_bandwidth (float, optional) – Bandwidth of the Gaussian smoothing function used during the KDE.
min_expression (float, optional) – A minimal expression threshold to report as local maximum regions of interest.
- Returns:
pseudocell_locations – A list of local maxima in a KDE of the data frame.
- Return type: