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,
  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,
  ...
)

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	Vector of conditions to be tested corresponding to each image.
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.
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.

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 Aug. 10, 2024, 12:08 p.m.