Package index
Compare two samples
The main function: the spatial correlation test and the spatial similarity for every gene, and the methods of its result.
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compareSpatial() - Compare the spatial expression patterns of genes between two samples
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print(<STcompareResult>)summary(<STcompareResult>)print(<summary.STcompareResult>)`[`(<STcompareResult>)as.data.frame(<STcompareResult>) - Methods for compareSpatial() results
Spatial correlation, legacy functions
The correlation functions of earlier versions. They reproduce the published analyses exactly.
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spatialCorrelationGeneExp() - Spatial correlation test for every gene of two samples
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spatialCorrelationGeneExpIterPermutations() - Spatial correlation test with more permutations for promising genes
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spatialCorrelationGeneExpWithinSample() - Spatial correlation test between pairs of genes of one sample
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spatialCorrelation() - Spatial correlation test of two vectors of values at the same locations
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viladomatCorrelation() - Spatially autocorrelated surrogates and permutation p-value for one direction
Visualization
Standard figures of a compareSpatial() result: one gene with its maps, similarity classes and statistics, and the overview of all genes. The legacy functions plot single genes from the results of the legacy functions.
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plotGene() - Standard figure of one gene in a compareSpatial() result
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plotOverview() - Overview figure of a compareSpatial() result
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linearRegression() - Plot a gene's values in two samples, coloured by similarity class
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pixelClass() - Map the similarity class of every pixel
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plotCorrelationGeneExp() - Plot a gene's values in two samples at the shared pixels
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savePlots() - Maps, pixel classes and scatter plot of genes, optionally saved as PDF
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spatialSimilarity() - Computes spatial similarity of gene expression between two SpatialExperiments.
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speKidney - Simulated Kidney SpatialExperiment Data
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simRanPatternRasts - Simulated Random Spatially Patterned Kidney Datasets