meta.table dumping

mdibl · Nov 21, 2024 · a1a0f88 · a1a0f88
1 parent e89319e
commit a1a0f88
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Showing 2 changed files with 20 additions and 3 deletions.
diff --git a/bin/Plotting.R b/bin/Plotting.R
@@ -216,6 +216,22 @@ if(toupper(params.MakeLoupe) == "TRUE"){
 message("Saving Seurat Object")
 SaveSeuratRds(MergedSO, file = paste0("08",params.ProjectName, "_FinalSO.rds"))
 
+# ╔════════════════════════╗
+# ╠═ Save Meta Data Table ═╣
+# ╚════════════════════════╝
+meta_table <- MergedSO@meta.data
+meta_table <- cbind(meta_table, as.data.table(MergedSO@reductions$pca@cell.embeddings))
+if (params.IntegrationMethod != "NULL"){
+    meta_table <- cbind(meta_table, MergedSO@reductions[[paste0("tsne.",params.IntegrationMethod)]]@cell.embeddings)
+    meta_table <- cbind(meta_table, MergedSO@reductions[[paste0("umap.",params.IntegrationMethod)]]@cell.embeddings)
+} else {
+    meta_table <- cbind(meta_table, MergedSO@reductions[["tsne.unintegrated"]]@cell.embeddings)
+    meta_table <- cbind(meta_table, MergedSO@reductions[["umap.unintegrated"]]@cell.embeddings)
+}
+write.csv(file = paste0("08_",params.ProjectName,"_MetaTable.tsv"), meta_table, col.names = T)
+
+
+
 # ╔═════════════════╗
 # ╠═ Save Log File ═╣
 # ╚═════════════════╝

diff --git a/modules/local/plotting/main.nf b/modules/local/plotting/main.nf
@@ -20,12 +20,13 @@ process DISPLAY_REDUCTION {
 
     output:
     tuple val(meta), path ("*_FinalSO.rds"), emit: rds
-    path("*Validation.log"),           emit: log
-    path("*.cloupe"),                  optional: true
+    path("*Validation.log"), emit: log
+    path("*.cloupe"), optional: true
     path("*.pdf")
-    path ("*FinalVersions.log"),                     emit: r_versions
+    path ("*FinalVersions.log"), emit: r_versions
     path('versions.yml'), emit: versions
     path("*Execution.log"), emit: exec
+    path("*_MetaTable.tsv"), emit: meta
 
     when:
     task.ext.when == null || task.ext.when