Garfield.plot.plot_markers

Garfield.plot.plot_markers(adata: AnnData, groupby: str, mks: DataFrame, n_genes: int = 5, kind: str = 'dotplot', remove_genes: list = [], **kwargs)

Plot markers for specific groups.

Parameters:

• adata (AnnData) – AnnData object containing expression data.

• groupby (str) – Column in adata.obs used for grouping cells.

• mks (DataFrame) – DataFrame containing marker statistics.

• n_genes (int, optional) – Number of top genes to plot per group. Default is 5.

• kind (str, optional) – Type of plot to create (‘dotplot’, ‘violin’, etc.). Default is ‘dotplot’.

• remove_genes (list, optional) – List of genes to exclude from the plot. Default is an empty list.

• **kwargs (dict) – Additional keyword arguments passed to the plotting function.

Returns:

Axes object of the plot or None if plotting in place.

Return type:

matplotlib.Axes or None