This tutorial demonstrates how to load data and the input files that SpaCCI need.

Required input data for SpaCCI analysis

SpaCCI requires two main input datasets:

  1. Gene Expression Data: A spot-level data frame with genes as row names and spot IDs as column names.
  2. Cell Type Proportion Data: A spot-level data frame with spot IDs as row names and cell type labels as column names.

With one correspond:

  1. Spatial Coordinates : A spot-level data frame with spot IDs as row names and c(“imagerow”,”imagecol”) as column names