Plotting: pl

Similar to scanpy, this module parallels some functions, but mainly for the core im.* functions to display the results of TMA masking, dearraying and segmentation. Some functions in tl.* also have a plotting function.

Images

These functions wrap spatialdata_plot into scanpy-like functions to display image, label and shapes data from a SpatialData object.

pl.image	Displays an Image element from the SpatialData object.
pl.mask_tma	Displays a labels element from the SpatialData object, such as the generated TMA masks.
pl.dearray_tma	Displays a shapes element from the SpatialData object, such as the generated TMA envelopes and cores.
pl.segment_tma	Displays a labels element from the SpatialData object, such as the cell segmentation results.
pl.preview_tma_segmentation	Displays a visual preview of the input data given to Cellpose for segmentation.

Tables

These functions display results from analyses involving AnnDatas / tables.

pl.cluster_scores

Plot the cluster stability scores from a clustering run.