Colon Spatial Transcriptomics Metadata

Source: R/data.R

Spot metadata for the colon Visium example dataset

st_meta

Format

A data.frame with 1,000 rows (spots) and 5 columns:

x

X coordinate in image pixels (imagecol)

y

Y coordinate in image pixels (imagerow)

array_row

Row position in the Visium array

array_col

Column position in the Visium array

cell_type

Cell type annotation (mock clusters for testing)

Details

The cell_type column contains mock cell type annotations generated by spatial k-means clustering. In real analysis, users should provide cell type annotations from deconvolution methods (e.g., RCTD, cell2location, SPOTlight) or manual annotation.

Cell type distribution in this example:

  • Epithelial: ~189 spots

  • Fibroblast: ~232 spots

  • Endothelial: ~174 spots

  • Immune: ~145 spots

  • Stromal: ~133 spots

  • Tumor: ~127 spots

Examples

# \donttest{
data(st_meta)

# View spot distribution
table(st_meta$cell_type)
#> 
#> Endothelial  Epithelial  Fibroblast      Immune     Stromal       Tumor 
#>         174         189         232         145         133         127 

# Plot spatial coordinates
plot(st_meta$x, st_meta$y, col = as.factor(st_meta$cell_type), pch = 16)

# }