Visualize cell fractions

This example demonstrates how to generate celltype quantification plots. These types of plots can be used to visually represent the number of cells that belong to a certain subset or condition.

import besca as bc
import pytest

# pytest.skip('Test is only for here as example and should not be executed')

# import dataset to workwith
adata = bc.datasets.Peng2019_processed()

quantify specific celllabels as a stacked barplot

bc.pl.celllabel_quant_stackedbar(
    adata, count_variable="Cell_type", subset_variable="Patient"
)

<AxesSubplot:ylabel='percentage'>

quantify number of cells belong to each condition in a specific subset

here each dot represents one Patient, the boxplots are grouped according to tissue type (Normal or Tumoral)

bc.pl.celllabel_quant_boxplot(
    adata,
    count_variable="Cell_type",
    subset_variable="Patient",
    condition_identifier="Type",
    plot_percentage=True,
)

<Figure size 800x400 with 1 Axes>

here you can also choose to plot total counts instead of percentages

bc.pl.celllabel_quant_boxplot(
    adata,
    count_variable="Cell_type",
    subset_variable="Patient",
    condition_identifier="Type",
    plot_percentage=False,
)

<Figure size 800x400 with 1 Axes>