getPairwise | R Documentation |

Get statistic from pairwise L curve of a single image.

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

`cells` |
A SummarizedExperiment 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. |

`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. |

`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. |

`imageIDCol` |
The name of the imageID column if using a SingleCellExperiment or SpatialExperiment. |

`cellTypeCol` |
The name of the cellType column if using a SingleCellExperiment or SpatialExperiment. |

`spatialCoordCols` |
The names of the spatialCoords column if using a SingleCellExperiment. |

Statistic from pairwise L curve of a single image.

```
data("diabetesData")
# Subset by imageID for fast example
selected_cells <- diabetesData[
, SummarizedExperiment::colData(diabetesData)$imageID == "A09"
]
pairAssoc <- getPairwise(selected_cells)
```

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