sample for generating a simple csv

script.r

library(GBCC.mcm)
library(SummarizedExperiment)
library(SpatialFeatureExperiment)
x = GBCC.mcm::process_mcmicro("input.h5ad")
expr_matrix <- assay(x, "X")
expr_df <- as.data.frame(t(expr_matrix))  # Transpose so cells are rows
# Get cell metadata
metadata <- as.data.frame(colData(x))
# Get spatial coordinates
coords <- as.data.frame(spatialCoords(x))
# Combine everything into one comprehensive table
combined_data <- cbind(
    cell_id = rownames(metadata),
    coords,
    metadata,
    expr_df
)
# Write to CSV
write.csv(combined_data, "spatial_expression_data.csv", row.names = FALSE)