stlearn.pl.QC_plot

stlearn.pl.QC_plot(adata: AnnData, library_id: Optional[str] = None, name: Optional[str] = None, data_alpha: float = 0.8, tissue_alpha: float = 1.0, cmap: str = 'Spectral_r', spot_size: tuple = (5, 40), show_color_bar: bool = True, show_size_legend: bool = True, show_axis: bool = False, cropped: bool = True, margin: int = 100, dpi: int = 150, output: Optional[str] = None) → Optional[AnnData][source]

QC plot for sptial transcriptomics data.

Parameters:

  • adata – Annotated data matrix.

  • library_id – Library id stored in AnnData.

  • data_alpha – Opacity of the spot.

  • tissue_alpha – Opacity of the tissue.

  • cmap – Color map to use.

  • spot_size – Size of the spot (min, max).

  • show_color_bar – Show color bar or not.

  • show_axis – Show axis or not.

  • show_size_legend – Show size legend or not.

  • name – Name of the output figure file.

  • output – Save the figure as file or not.

  • copy – Return a copy instead of writing to adata.

Return type:

Nothing