SpicyResults-class | R Documentation |

Performs spatial tests on spatial cytometry data.

```
spicy(
cells,
condition,
subject = NULL,
covariates = NULL,
from = NULL,
to = NULL,
imageIDCol = "imageID",
cellTypeCol = "cellType",
spatialCoordCols = c("x", "y"),
alternateResult = NULL,
verbose = FALSE,
weights = TRUE,
weightsByPair = FALSE,
weightFactor = 1,
window = "convex",
window.length = NULL,
BPPARAM = BiocParallel::SerialParam(),
sigma = NULL,
Rs = NULL,
minLambda = 0.05,
edgeCorrect = TRUE,
includeZeroCells = FALSE,
...
)
```

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

`condition` |
A character specifying which column which contains the condition or 'Surv' objects |

`subject` |
Vector of subject IDs corresponding to each image if cells is a data frame. |

`covariates` |
Vector of covariate names that should be included in the mixed effects model as fixed effects. |

`from` |
vector of cell types which you would like to compare to the to vector |

`to` |
vector of cell types which you would like to compare to the from vector |

`imageIDCol` |
The image ID if using SingleCellExperiment. |

`cellTypeCol` |
The cell type if using SingleCellExperiment. |

`spatialCoordCols` |
The spatial coordinates if using a SingleCellExperiment. |

`alternateResult` |
An pairwise association statistic between each combination of celltypes in each image. |

`verbose` |
logical indicating whether to output messages. |

`weights` |
logical indicating whether to include weights based on cell counts. |

`weightsByPair` |
logical indicating whether weights should be calculated for each cell type pair. |

`weightFactor` |
numeric that controls the convexity of the weight function. |

`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. |

`BPPARAM` |
A BiocParallelParam object. |

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

`Rs` |
A vector of radii that the measures of association should be calculated. If NULL, Rs = c(20, 50, 100) is specified by default. |

`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. |

`...` |
Other options. |

Data frame of p-values.

```
data("diabetesData")
# Test with random effect for patient on a pairwise combination of cell
# types.
spicy(diabetesData,
condition = "stage", subject = "case",
from = "Tc", to = "Th"
)
# Test all pairwise combinations of cell types without random effect of
# patient.
## Not run:
spicyTest <- spicy(diabetesData, condition = "stage", subject = "case")
## End(Not run)
# Test all pairwise combination of cell types with random effect of patient.
## Not run:
spicy(diabetesData, condition = "condition", subject = "subject")
## End(Not run)
```

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.