SpicyResults-class | R Documentation |
Performs spatial tests on spatial cytometry data.
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,
...
)
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 |
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)
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