Using SpatialExperiment and plotSpatial in RStudio to visualize my spatial neighbours in the IMC data. Unfortunately, it only gives a black square (without any errors or warnings).
What would be the reason? See script:

counts <- as.matrix(all_cells_combined[,  c(1:5)])

# Create the DataFrame for spatial coordinates:
#with modified coords
meta_data <- data.frame(
  x = all_cells_combined$`centroid-1`,
  y = all_cells_combined$`centroid-0`,
  Cell_id = all_cells_combined$Cell_id,
  roi_id = all_cells_combined$ROI,
  sample_id = all_cells_combined$patient
)

# Make sure the dimensions of assay and colData align correctly
# by transposing the 'y' matrix if needed:
if (ncol(counts) != ncol(meta_data)) {
  counts <- t(counts)
}

# Create the SpatialExperiment object:
spe <- SpatialExperiment(
  assay = counts, 
  colData = meta_data, 
  spatialCoordsNames = c("x", "y")
)


pheno <- data.frame(all_cells_combined$phenotype)
colnames(pheno) <- c("pheno")
colData(spe) <- cbind(colData(spe), pheno)


#spatial analysis
spe <- buildSpatialGraph(spe, img_id = "roi_id", type = "knn", k=10, coords = c("x", "y"))
spe <- buildSpatialGraph(spe, img_id = "roi_id", type = "expansion", threshold = 20, coords = c("x", "y")) 

duplicated_ids <- duplicated(spe$sample_id)
print(spe$sample_id[duplicated_ids])
unique(spe$sample_id)

png("file.png", 
   width = 20, height = 20, res = 300, units = "in")

plotSpatial(spe[,spe$roi_id == "x1"],
            coords = c("x", "y"),
            node_color_by = "pheno",
            node_size_fix = 1.5,
            img_id = "roi_id", 
            draw_edges = TRUE, 
            colPairName = "knn_interaction_graph", 
            nodes_first = FALSE,
            edge_color_fix = "white") + #scale_color_manual(values = color_mapping) +
  theme(
    panel.background = element_rect(fill = "black"),
    legend.position = "none",
    panel.grid = element_blank(),
    axis.text = element_blank(),
    axis.ticks = element_blank(),
    axis.title = element_blank()
  )

dev.off()

I have checked the coordinates etc. and those are correct.

counts <- countInteractions(spe,
                            group_by = "roi_id",
                            label = "pheno",
                            colPairName = "knn_interaction_graph",
                            method = c("classic"),
                            patch_size = NULL
) %>% as.data.frame()

I have done this after ‘plotting’ and it works/looks adequate. So that’s why I am confused as to why it wouldn’t plot properly.

Many thanks in advance!