## ----include=TRUE, results="hide", message=FALSE, warning=FALSE---------------

library(MultiAssayExperiment)
library(SpatialExperiment)
library(SingleCellMultiModal)


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SingleCellMultiModal::seqFISH(DataType="mouse_visual_cortex", 
                        modes="*", dry.run=TRUE, version="2.0.0")


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mae <- SingleCellMultiModal::seqFISH(DataType="mouse_visual_cortex", 
                        modes="*", dry.run=FALSE, version="2.0.0")
mae

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experiments(mae)

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rownames(mae)

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sampleMap(mae)

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experiments(mae)$scRNAseq

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head(assay(mae, "scRNAseq"))[,1:4]

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experiments(mae)$seqFISH

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head(assay(mae, "seqFISH"))[,1:4]

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(sc <- spatialCoords(experiments(mae)$seqFISH))

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fakeCoords <- cbind(sc[,c(1:3)], sc[,3])
colnames(fakeCoords)[4] <- "y"
spatialCoords(experiments(mae)$seqFISH) <- fakeCoords
spatialCoords(experiments(mae)$seqFISH)

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spatialCoordsNames(experiments(mae)$seqFISH)

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mae <- SingleCellMultiModal::seqFISH(DataType="mouse_visual_cortex", 
                        modes="*", dry.run=FALSE, version="1.0.0")
mae

## -----------------------------------------------------------------------------
sessionInfo()