example XenSCE instance based on pancreas subset from SFEData XeniumOutput

example XenSCE instance based on pancreas subset from SFEData XeniumOutput

panc_sub

Format

XenSCE

Examples

data(panc_sub)
head(panc_sub)
#> class: XenSCE 
#> dim: 6 6272 
#> metadata(0):
#> assays(1): counts
#> rownames(6): ENSG00000121270 ENSG00000130234 ... ENSG00000163017
#>   ENSG00000042980
#> rowData names(1): symbol
#> colnames(6272): abclkehb-1 abcnopgp-1 ... odmgoega-1 odmgojlc-1
#> colData names(12): cell_id x_centroid ... nucleus_area sample_id
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : x_centroid y_centroid
#> imgData names(0):
#> Geometry elements:
#>               nrow ncol
#> transcripts 367354   11
#> cellbounds  156512    4
#> nucbounds   154156    4
plot(panc_sub$x_centroid, panc_sub$y_centroid, pch="." , cex=1.5, xlab="x", ylab="y", main="cell centroids")