FACSPy.pl.cluster_frequency

FACSPy.pl.cluster_frequency(adata, gate, cluster_key, cluster, normalize=False, groupby=None, splitby=None, cmap=None, order=None, stat_test='Kruskal', figsize=(3, 3), return_dataframe=False, return_fig=False, ax=None, show=True, save=None, **kwargs)

Plots the cluster frequency per cluster as a combined strip-/boxplot.

Parameters:

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

• gate (str) – The gate to be analyzed, called by the population name. This parameter has a default stored in fp.settings, but can be superseded by the user.

• cluster_key (str) – The .obs column where the cluster information is stored.

• cluster (str) – Specifies the cluster to be analyzed.

• normalize (bool) – If True, normalizes the frequencies to the total amount of cells. If False, plots the cell counts per cluster and group.

• groupby (Optional[Union`[:py:class:`list[str], str]]) – The parameter to group the x-axis.

• 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[list[str]]) – specifies the order of x-values.

• stat_test (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.

• kwargs – keyword arguments ultimately passed to sns.stripplot.

Return type:

Optional[Figure, Axes, DataFrame]]

Returns:

• If show==False a Axes

• If return_fig==True a Figure

• If return_dataframe==True a pandas.DataFrame containg the data used for plotting

Examples

import FACSPy as fp

dataset = fp.mouse_lineages()

fp.settings.default_gate = "CD45+"
fp.settings.default_layer = "transformed"

fp.tl.pca(dataset)
fp.tl.neighbors(dataset)
fp.tl.leiden(dataset)
fp.pl.cluster_frequency(
    dataset,
    cluster_key = "CD45+_transformed_leiden",
    cluster = "0",
    groupby = "organ"
)