Download Example Data
The following are the example dataset for the SpaCCI tutorial.
1. Seurat Data for Tutorial
For the Seurat object used in the tutorial, please first install package and load the data as the following
library(SpaCCI)
# Load the tutorial data
load(system.file("extdata", "Tutorial_example_data.rda", package = "SpaCCI"))
After loading Tutorial_example_data.rda, the following objects should be available:
Example_Seurat: A Seurat object containing 10X Visium data with an associated image.cell_prop_df: A data frame containing spot-level cell type proportions.interest_region_Spot_IDs: Spot IDs for conducting “regional” analysis.
2. Non Seurat Data for Tutorial
If NOT using the Seurat object, please also first download the following data file.
- Gene Expression Data: A spot-level data frame with genes as row names and spot IDs as column names.
- Cell Type Proportion Data: A spot-level data frame with spot IDs as row names and cell type labels as column names.
- Spatial Coordinates : A spot-level data frame with spot IDs as row names and
c("imagerow","imagecol")as column names.
For regional analysis, please also load the data as following to obtain the interest_region_Spot_IDs:
library(SpaCCI)
# Load the tutorial data
load(system.file("extdata", "Tutorial_example_data.rda", package = "SpaCCI"))
3. Real 10X Visium Data
GSE233254: Contains the 10X Visium data.
GSE233293: Contains the RCTD(Robust Cell Type Deconvolution) of the 10X Visium data.