Basic¶

cell_components¶

class spatialtis.cell_components(data, **kwargs)[source]¶

Count the proportion of each types of cells in each group

Parameters

class spatialtis.cell_co_occurrence(data, **kwargs)[source]¶

The likelihood of two type of cells occur simultaneously in a ROI

Parameters

class spatialtis.cell_density(data, ratio=1.0, **kwargs)[source]¶

Calculating cell density in each ROI

The size of each ROI will be auto-computed, it’s the area of convex hull of all the cells in a ROI

Parameters

data (anndata._core.anndata.AnnData) – AnnData object to perform analysis
ratio (Union[int, float]) – The ratio between the unit used in your dataset and real length unit, default is 1.0; ratio = Dataset unit / real length unit; For example, if the resolution of your dataset is 1μm, but you want to use 1mm as unit, then you should set the ratio as 0.001, 1 pixels represent 0.001mm length.
**kwargs – Pass to spatialtis.abc.AnalysisBase

class spatialtis.cell_morphology(data, metric_key=None, **kwargs)[source]¶

Cell morphology variation between different groups

Parameters

data (anndata._core.anndata.AnnData) – AnnData object to perform analysis
metric_key (Optional[str]) – Which key in AnnData.obs to measure morphology (Default: eccentricity key)
**kwargs – Pass to spatialtis.abc.AnalysisBase