SpatialExperiment-class {SpatialExperiment} | R Documentation |
The SpatialExperiment class is designed to represent 10x Visium spatial Gene Expression data. It inherits from the SingleCellExperiment class and is used in the same manner. In addition, the class supports the integration with 10x Visium spatial coordinates and its scale factors.
SpatialExperiment(..., spatialCoords = data.frame())
... |
arguments to be passed to the |
spatialCoords |
the spatial coordinates |
none
Dario Righelli
## building random seqFISH data coordinates fishCoordinates <- data.frame(Cell_ID=paste0("cell",c(1:30)), Irrelevant=100, x=sample(c(-4000:4000), size=30, replace=TRUE), y=sample(c(-4000:4000), size=30, replace=TRUE)) ## building random seqFISH cell labels fishCellLabels <- data.frame(Cell_ID=paste0("cell",c(1:30)), class="neuron", classID=sample(c(0:5), size=30, replace=TRUE)) ## building random seqFISH count matrix fishCounts <- matrix(sample(0:100, size=(30*30), replace=TRUE), nrow=30, ncol=30, dimnames=list(paste0("gene",c(1:30)), paste0("cell",c(1:30)))) ## creating SpatialExperiment object se <- SpatialExperiment(rowData=rownames(fishCounts), colData=fishCellLabels, assays=SimpleList(counts=as.matrix(fishCounts)), spatialCoords=fishCoordinates)