compute_persistence-checkpoint

Functions

run_persistence(data[, p, m, mesh_type, sensitivity, ...])

Computes spatial structure scores for all variables in a spatial 'omics dataset.

Module Contents

compute_persistence-checkpoint.run_persistence(data: pandas.DataFrame, p: int = 2, m: float = 0.1, mesh_type: str = 'hexagonal', sensitivity: float = 1, metrics_storage_location: str = None, diagrams_storage_location: str = None, log_storage_location: str = None, notes: str = None, return_metrics: bool = True, return_diagrams: bool = False)

Computes spatial structure scores for all variables in a spatial ‘omics dataset.

Takes in expression and co-ordinate data for a set of wells from a single tissue sample and computes the Coefficient of spatial structure (CoSS) for each gene. Optionally stores spatial metrics (norms, ratios, ranks, and SVG calls) and persistence diagrams in user-specified locations.

Parameters:

  • data (pd.DataFrame) –

    pandas DataFrame of the form

    x , y , gene1 , gene2, … , geneN . . . . . . . . . .

    where (x, y) are the co-ordinates of each well, and genei is the expression of gene i in each well.

  • p (float, default=2) – Specifies which norm of the 0D persistence diagram to use as the CoSS. Should lie in [0,infinity).

  • m (float, default=0.1) – Specifies the probability mass threshold to use in distance to measure computation. Should lie in (0,1).

  • mesh_type (str, default='hexagonal') – Type of mesh that the well co-ordinates lie on. Allowed values are “hexagonal” or “square”.

  • sensitivity (float, default=1) – Controls the behaviour of the automatic CoSS threshold selection for declaring a gene as spatially variable.

  • metrics_storage_location (str, default=None) – Filepath specifiying where to store metrics csv file.

  • diagrams_storage_location (str, default=None) – Filepath specifiying where to store the dictionary of persistence diagrams for each gene. Stored as a pickle file.

  • log_storage_location (str, default=None) – Filepath specifying where to record details of persistence computation. Stored as a text file.

  • notes (str, default=None) – Extra text to be appended on to the log.

  • return_metrics (bool, default=True) – Whether to return the metrics data frame. If return_metrics=True and return_diagrams=True, both objects will be reutrned in the order (metrics, diagrams).

  • return_diagrams (bool, default=True) – Whether to return persistence diagrams what objects to return. If return_metrics=True and return_diagrams=True, both objects will be reutrned in the order (metrics, diagrams).

Returns:

  • pd.DataFrame – Data frame contaning CoSS and other metrics for each gene.

  • List[d.Diagram] – Lost of persistence diagrams for each gene, indexed by gene name (taken from the column names of the input data frame).