squidpy.experimental.pl.tiling_qc

squidpy.experimental.pl.tiling_qc(sdata, labels_key, qc_key=None, score_col='nhood_outlier_fraction', cmap='RdYlGn_r', figsize=None)[source]

Plot labels coloured by their tiling-artifact score.

Uses spatialdata_plot to render the label element coloured by the chosen QC score from the linked table. If tile-boundary artifacts are present the tile grid emerges as lines of high-scoring cells.

Parameters:

  • sdata (SpatialData) – SpatialData object (must contain the QC table).

  • labels_key (str) – Key in sdata.labels with the segmentation mask.

  • qc_key (str | None) – Key in sdata.tables with the QC AnnData. Defaults to "{labels_key}_qc".

  • score_col (Literal['nhood_outlier_fraction', 'smoothed_cut_score', 'cut_score', 'max_straight_edge_ratio', 'cardinal_alignment_score', 'is_outlier']) – Which .obs column to colour by. One of "nhood_outlier_fraction", "smoothed_cut_score", "cut_score", "max_straight_edge_ratio", "cardinal_alignment_score", "is_outlier".

  • cmap (str) – Matplotlib colormap name.

  • figsize (tuple[float, float] | None) – Figure size passed to spatialdata.SpatialData.pl.show.

Return type:

None