max_counts

besca.pl.max_counts(adata, max_counts=10000, ax=None, figsize=None)[source]

visualize maximum UMI counts per cell threshold.

this function generates a knee-plot visualizing a given min_cells cutoff when given an adata object

Parameters:

  • adata (AnnData) – The annotated data matrix.

  • max_counts (int | default = 10000) – visualize the chosen maximum UMI counts cutoff

  • ax (axes | default = None) – pass the axes class to which your figure should be added

  • figsize ((width, height) or None | default = None) – optional parameter to define the figure size of the plot that is to be generated

Returns:

Figure is displayed

Return type:

None

Example

Generates a “knee-plot” for a maximum UMI count of 6500 for the example dataset. >>> import besca as bc >>> import matplotlib.pyplot as plt >>> adata = bc.datasets.simulated_pbmc3k_raw() >>> max_counts = 6500 >>> fig, ax1 = plt.subplots(1) >>> bc.pl.max_counts(adata, max_counts = max_counts, ax = ax1)