Move species count to analysis

R/analyze.R

@@ -75,13 +75,23 @@ analyze <- function(preset, progress = NULL) {
             total_progress <- total_progress + 1 / method_count
         }
 
-        if (!is.null(progress)) {
-            progress(1.0)
-        }
+        # Count included species from the preset per gene.
+        genes_n_species <- geposan::distances[
+            species %chin% preset$species_ids,
+            .(n_species = .N),
+            by = "gene"
+        ]
 
-        results
+        setkey(genes_n_species, "gene")
+
+        # Return the results for genes with enough species.
+        results[genes_n_species[gene, n_species] >= preset$min_n_species]
     })
 
+    if (!is.null(progress)) {
+        progress(1.0)
+    }
+
     structure(
         list(
             preset = preset,