FACSPy.pl.cofactor_distribution

FACSPy.pl.cofactor_distribution(adata, marker, groupby, splitby=None, cmap=None, order=None, stat_test='Kruskal', figsize=(3, 3), return_dataframe=False, return_fig=False, ax=None, show=True, save=None)

Plots the cofactor distribution of specific channels.

Parameters:

• adata (AnnData) – The anndata object of shape n_obs x n_vars where rows correspond to cells and columns to the channels.

• marker (str) – The channel to be displayed. Has to be in adata.var_names.

• groupby (str) – controls the x axis and the grouping of the data points.

• splitby (Optional[str]) – The parameter controlling additional split along the groupby-axis.

• cmap (Optional[str]) – Sets the colormap for plotting. Can be continuous or categorical, depending on the input data. When set, both seaborns ‘palette’ and ‘cmap’ parameters will use this value.

• order (Optional[Union`[:py:class:`list[str], str]]) – specifies the order of x-values.

• stat_test (Optional[str]) – Statistical test that is used for the p-value calculation. One of Kruskal and Wilcoxon. Defaults to Kruskal.

• figsize (tuple[float, float]) – Contains the dimensions of the final figure as a tuple of two ints or floats.

• return_dataframe (bool) – If set to True, returns the raw data that are used for plotting as a dataframe.

• return_fig (bool) – If set to True, the figure is returned.

• ax (Optional[Axes]) – A Axes created from matplotlib to plot into.

• show (bool) – Whether to show the figure. Defaults to True.

• save (Optional[str]) – Expects a file path including the file name. Saves the figure to the indicated path. Defaults to None.

Return type:

Optional[Figure, Axes, DataFrame]]

Returns:

• If show==False a Axes

• If return_fig==True a Figure

• If return_dataframe==True a DataFrame containing the data used for plotting

Examples

import FACSPy as fp

dataset = fp.mouse_lineages()

fp.pl.cofactor_distribution(
    dataset,
    marker = "B220",
    groupby = "organ"
)