convPairs: Converts colPairs object into an abundance matrix based on...

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

Converts colPairs object into an abundance matrix based on number of nearby interactions for every cell type.

Description

Converts colPairs object into an abundance matrix based on number of nearby interactions for every cell type.

Usage

convPairs(cells, colPair, imageID = "imageID", cellType = "cellType")

Arguments

cells	A SingleCellExperiment that contains objects in the colPairs slot.
colPair	The name of the object in the colPairs slot for which the dataframe is constructed from.
imageID	The image ID if using SingleCellExperiment.
cellType	The cell type if using SingleCellExperiment.

Value

Matrix of abundances

Examples

data("diabetesData")
images <- c("A09", "A11", "A16", "A17")
diabetesData <- diabetesData[
  , SummarizedExperiment::colData(diabetesData)$imageID %in% images
]

diabetesData_SPE <- SpatialExperiment::SpatialExperiment(diabetesData,
  colData = SummarizedExperiment::colData(diabetesData)
)
SpatialExperiment::spatialCoords(diabetesData_SPE) <- data.frame(
  SummarizedExperiment::colData(diabetesData_SPE)$x,
  SummarizedExperiment::colData(diabetesData_SPE)$y
) |>
  as.matrix()

SpatialExperiment::spatialCoordsNames(diabetesData_SPE) <- c("x", "y")

diabetesData_SPE <- imcRtools::buildSpatialGraph(diabetesData_SPE,
  img_id = "imageID",
  type = "knn",
  k = 20,
  coords = c("x", "y")
)

pairAbundances <- convPairs(diabetesData_SPE,
  colPair = "knn_interaction_graph"
)

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