Drop graph when only 1 cell is left in sample as the graph is meaning…

…less, #58
pachterlab · Nov 20, 2024 · be522f7 · be522f7
1 parent 65f5b8e
commit be522f7
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diff --git a/R/subset.R b/R/subset.R
@@ -145,6 +145,12 @@ setMethod(
             )
             for (s in which(samples_subset)) {
                 j_sample <- old_sample_compare[[s]] %in% new_sample_colnames[[s]]
+                if (sum(j_sample) == 1) {
+                    message("Only 1 column left in sample ", sample_ids[[s]],
+                            ", graphs are meaningless, dropping graphs.")
+                    graphs_sub[[s]] <- list(row = NULL, col = NULL, annot = NULL)
+                    next
+                }
                 for (m in seq_len(2)) { # Not subsetting annotGraphs
                     # Not sure what to do differently with rowGraphs yet
                     for (g in seq_along(graphs_sub[[s]][[m]])) {

diff --git a/tests/testthat/test-subset.R b/tests/testthat/test-subset.R
@@ -81,6 +81,17 @@ test_that("Subset the graph when distance-based edge weights are used", {
     )
 })
 
+test_that("When only one cell/spot is left in a sample after subsetting", {
+    expect_message(sfe1 <- sfe_visium[,1:6], "graphs are meaningless, dropping graphs")
+    expect_null(colGraphNames(sfe1, sample_id = "sample02"))
+})
+
+test_that("When only one cell is left, option reconstruct", {
+    withr::local_options(SFE_graph_subset = FALSE)
+    expect_message(sfe1 <- sfe_visium[,1:6], "graphs are meaningless, dropping graphs")
+    expect_null(colGraphNames(sfe1, sample_id = "sample02"))
+})
+
 test_that("Warning message and dropping graphs when reconstruction info is unavailable", {
     withr::local_options(SFE_graph_subset = FALSE)
     # Remove one item from sample02