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Computes spatial similarity of gene expression between two SpatialExperiments.

spatialSimilarity.Rd

This function calculates the spatial similarity of gene expression patterns between two SpatialExperiment objects based on thresholding and fold-change criteria. Similarity is defined as the proportion of pixels where the fold change in gene expression falls within a specified range.

Usage

spatialSimilarity(
  input,
  t1 = NULL,
  t2 = NULL,
  minQuantile = 0.05,
  minPixels = 0.1,
  foldChange = 1,
  assayName = NULL
)

Arguments

input

List of two SpatialExperiment objects. The first element corresponds to the first spatial experiment (`x`), and the second to the second spatial experiment (`y`). Similarity is computed as the proportion of pixels satisfying: `-b <= log2(y/x) <= b` for each gene, where `b = 1` as default

t1

numeric: Gene expression threshold for the first spatial experiment (`x`). Only pixels with values greater than t1 or t2 are used to calculate similarity score. Default is NULL. If no value is supplied for t1, then each gene will have a threshold set as by minQuantile.

t2

numeric: Gene expression threshold for the second spatial experiment (`y`). Only pixels with values greater than t1 or t2 are used to calculate similarity score. Default is NULL. If no value is supplied for t2, then each gene will have a threshold set as by minQuantile.

minQuantile

numeric: Gene expression minimum quantile threshold to use if t1 and t2 are not supplied. Default is 0.05.

minPixels

numeric: Pixels minimum threshold. If less than this percentage of pixels meet the gene expression minimum threshold, then a spatial similarity score is not calculated for this gene and the function returns `NA`. Default is 0.1.

foldChange

numeric: Fold-change threshold defining similarity in gene expression across spatial locations. Default is 1.

assayName

A character string or numeric specifying the assay in the Spatial Experiment to use. Default is NULL. If no value is supplied for assayName, then the first assay is used as a default

Value

A list containing:

similarityTable

A data frame with the following columns:

  • geneGene name.

  • percentSimilarityPercentage of similar pixels for the gene.

  • percentDissimilarityXPercentage of pixels for which log2(y/x) < -foldChange.

  • percentDissimilarityYPercentage of pixels for which log2(y/x) > foldChange.

  • similarPixelIDList of pixel IDs classified as similar.

  • dissimilarPixelIDXList of pixel IDs for log2(y/x) < -foldChange.

  • dissimilarPixelIDYList of pixel IDs for log2(y/x) > foldChange.

  • numPixelInThreshNumber of pixels above the threshold in both experiments.

  • pixelIDInThreshList of pixel IDs above the threshold.

  • numPixelOutThreshNumber of pixels below the threshold.

  • pixelIDOutThreshList of pixel IDs below the threshold.

  • t1Threshold value for this gene in first spatial experiment.

  • t2Threshold value for this gene in second spatial experiment.

pixelLogTransformation

A data frame containing log-transformed fold-change values for each gene.

parameters

A list of input parameters used in the computation.

Examples

data(speKidney)
##### Rasterize to get pixels at matched spatial locations #####
rastKidney <- SEraster::rasterizeGeneExpression(speKidney,
               assay_name = 'counts', resolution = 0.2, fun = "mean",
               BPPARAM = BiocParallel::MulticoreParam(), square = FALSE)

s <- spatialSimilarity(list(rastKidney$A, rastKidney$C))