Data set consists of spatial transcriptomics data from a mouse embryo. There are three samples, for each we have gene expression data (351 genes), spatial coordinates on the two-dimensional spatial plane, and cell type labels. Sample 1 contains 19451 cells, sample 2 contains 14891 cells and sample 3 contains 23194 cells. We have randomly sampled 20% of the cells from each of these datasets for the vignette and examples to stop the data being too large. After the random sampling, we have 3848 cells in sample 1, 2986 cells in sample 2 and 4607 cells in sample 3.
Format
sample1_exprs has a row for each cell in sample 1 and a
column for the
expression level of each gene. sample1_coords has a row for each
cell in sample 1
and a column for its position in each of the two spatial axes.
sample1_cell_types
a vector whose i'th entry contains the cell type of the i'th cell of sample
1.
sample2_exprs has a row for each cell in sample 2 and a column
for the expression
level of each gene. sample2_coords has a row for each cell in
sample 2 and a column
for its position in each of the two spatial axes. sample2_cell_types
a vector whose
i'th entry contains the cell type of the i'th cell of sample 2.
sample3_exprs has
a row for each cell in sample 3 and a column for the expression level of
each gene.
sample3_coords has a row for each cell in sample 3 and a column
for its position
in each of the two spatial axes. sample3_cell_types a vector,
whose i'th entry
contains the cell type of the i'th cell of sample 3.
Source
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis, Nature Biotechnology, 2022. Webpage: https://www.nature.com/articles/s41587-021-01006-2