sample for generating a simple csv

script.r

library(GBCC.mcm)
library(SummarizedExperiment)
library(SpatialFeatureExperiment) # includes localResults method
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
)
# extract the "hot/coldspot statistics (Getis-Ord G*) as Z-score for each protein"
locg = localResults(x)$localG
dlocg = as.data.frame(locg) # undo the 'nesting'
kp = grep("Z.G", colnames(dlocg))  # keep only the Z-scores
dl = dlocg[,kp]
colnames(dl) = gsub("\\.i\\.", "", colnames(dl))  # trim the names
combined_data = cbind(combined_data, dl) # the trailing 27 columns have names [protein].Z.G
# Write to CSV
write.csv(combined_data, "spatial_expression_data.csv", row.names = FALSE)