getPairwise | R Documentation |

Get statistic from pairwise L curve of a single image.

getPairwise( cells, from = NULL, to = NULL, dist = NULL, window = "convex", window.length = NULL, Rs = c(20, 50, 100), sigma = NULL, minLambda = 0.05, fast = TRUE, edgeCorrect = TRUE, includeZeroCells = TRUE, BPPARAM = BiocParallel::SerialParam(), imageID = "imageID", cellType = "cellType", spatialCoords = c("x", "y") )

`cells` |
A SegmentedCells or data frame that contains at least the variables x and y, giving the location coordinates of each cell, and cellType. |

`from` |
The 'from' cellType for generating the L curve. |

`to` |
The 'to' cellType for generating the L curve. |

`dist` |
The distance at which the statistic is obtained. |

`window` |
Should the window around the regions be 'square', 'convex' or 'concave'. |

`window.length` |
A tuning parameter for controlling the level of concavity when estimating concave windows. |

`Rs` |
A vector of the radii that the measures of association should be calculated. |

`sigma` |
A numeric variable used for scaling when fitting inhomogeneous L-curves. |

`minLambda` |
Minimum value for density for scaling when fitting inhomogeneous L-curves. |

`fast` |
A logical describing whether to use a fast approximation of the inhomogeneous L-curves. |

`edgeCorrect` |
A logical indicating whether to perform edge correction. |

`includeZeroCells` |
A logical indicating whether to include cells with zero counts in the pairwise association calculation. |

`BPPARAM` |
A BiocParallelParam object. |

`imageID` |
The imageID if using a SingleCellExperiment or SpatialExperiment. |

`cellType` |
The cellType if using a SingleCellExperiment or SpatialExperiment. |

`spatialCoords` |
The spatialCoords if using a SingleCellExperiment or SpatialExperiment. |

Statistic from pairwise L curve of a single image.

data("diabetesData") pairAssoc <- getPairwise(diabetesData[1,])

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