A seeded toy dataset of 20 genes across 480 cells from 6 samples (three
Responders, three Non-responders) with three cell types (A, B, C) laid out on
a 500 x 500 field. Cell type B is concentrated in the right of the field, and
a neighbourhood-dependent signal is planted: gene G1 is up-regulated in the
index cell type A, in Responders, in proportion to the local density of the
niche cell type B. Used throughout the examples and vignette.
Usage
data(toySpiDE)Format
A SpatialExperiment
with a counts assay and colData
columns sample_id, condition, cell_type, Age, Area, and nCount.
Examples
data(toySpiDE)
toySpiDE
#> class: SpatialExperiment
#> dim: 20 480
#> metadata(0):
#> assays(1): counts
#> rownames(20): G1 G2 ... G19 G20
#> rowData names(0):
#> colnames(480): cell1 cell2 ... cell479 cell480
#> colData names(9): sample_id condition ... Area nCount
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : x y
#> imgData names(0):