chrysalis.plot_samples

chrysalis.plot_samples(adata: AnnData, rows: int, cols: int, dim: int, selected_comp: Union[int, str] = 'all', sample_col: str = 'sample', suptitle: Optional[str] = None, plot_size: float = 4.0, show_title: bool = True, spot_size=2, rotation=0, **plot_kw)

Visualize multiple samples from an AnnData object integrated with chrysalis.integrate_adatas in a single figure.

For details see chrysalis.plot. Individual compartments can be visualized instead of maximum intensity projection using ‘selected_comp’.

Parameters:

• adata – The AnnData data matrix of shape n_obs × n_vars. Rows correspond to cells and columns to genes.

• rows – Number of rows for subplots.

• cols – Number of columns for subplots.

• dim – Number of components to visualize.

• selected_comp – Show only the selected compartment if specified.

• sample_col – The .obs column storing the sample_id information, ‘sample’ by default.

• suptitle – Add suptitle to the figure.

• plot_size – Height and width of the individual subplots.

• show_title – Show title using labels from the .obs column defined using sample_col.

• spot_size – Adjust the final spot size.

• rotation – Rotate markers for alternative lattice arrangements.

• plot_kw – chrysalis.plot keyword arguments.