spicy: Performs spatial tests on spatial cytometry data.

In ellispatrick/spicyR: Spatial analysis of in situ cytometry data

Performs spatial tests on spatial cytometry data.

Description

Performs spatial tests on spatial cytometry data.

Usage

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

Arguments

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.
imageID	The name of the imageID column if using a SingleCellExperiment or SpatialExperiment.
cellType	The name of the cellType column if using a SingleCellExperiment or SpatialExperiment.
spatialCoords	The names of the spatialCoords column if using a SingleCellExperiment.
r	A vector of the radii that the measures of association should be calculated over.
sigma	A numeric variable used for scaling when fitting inhomogenous L-curves.
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.
alternateResult	A pairwise association statistic between each combination of celltypes in each image.
cores	Number of cores to use for parallel processing or a BiocParallel MulticoreParam or SerialParam object.
minLambda	Minimum value density for scaling when fitting inhomogeneous L-curves.
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.
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.
verbose	logical indicating whether to output messages.
BPPARAM	{DEPRECATED} A BiocParallel MulticoreParam or SerialParam object.
imageIDCol	{DEPRECATED} The name of the imageID column if using a SingleCellExperiment or SpatialExperiment.
cellTypeCol	{DEPRECATED} The name of the cellType column if using a SingleCellExperiment or SpatialExperiment.
spatialCoordCols	{DEPRECATED} The names of the spatialCoords column if using a SingleCellExperiment.
nCores	{DEPRECATED} Number of cores to use for parallel processing or a BiocParallel MulticoreParam or SerialParam object.
Rs	{DEPRECATED} A vector of the radii that the measures of association should be calculated over.
...	Other options

Value

Data frame of p-values.

Examples

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)

ellispatrick/spicyR documentation built on Dec. 20, 2024, 10:50 a.m.