Expand UpdateSeuratPrototype

Author: bbimber

singlecell/resources/chunks/CalculateTcrRepertoireStats.R

@@ -10,7 +10,9 @@ Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKe
 for (datasetId in names(seuratObjects)) {
   printName(datasetId)
   seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
-  df <- Rdiscvr::CalculateAndStoreTcrRepertoireStats(seuratObj)
+
+  outputFile <- gsub(seuratObjects[[datasetId]], pattern = '.rds', replacement = '.tcrStats.txt')
+  df <- Rdiscvr::CalculateAndStoreTcrRepertoireStats(seuratObj, outputFile = outputFile)
 
   # Cleanup
   rm(seuratObj)

singlecell/resources/chunks/UpdateSeuratPrototype.R

@@ -7,6 +7,12 @@ if (!file.exists(netRc)) {
 invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc))
 Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
 
+if (Sys.getenv('SEURAT_MAX_THREADS') != '') {
+  nCores <- Sys.getenv('SEURAT_MAX_THREADS')
+} else {
+  nCores <- 1
+}
+
 for (datasetId in names(seuratObjects)) {
   printName(datasetId)
   seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
@@ -34,6 +40,20 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- Rdiscvr::ClassifyTNKByExpression(seuratObj)
   }
 
+  if (saveRepertoireStats) {
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+    outputFile <- gsub(seuratObjects[[datasetId]], pattern = '.rds', replacement = '.tcrStats.txt')
+    df <- Rdiscvr::CalculateAndStoreTcrRepertoireStats(seuratObj, outputFile = outFile)
+  }
+
+  if (scoreActivation) {
+    seuratObj <- RIRA::PredictTcellActivation(seuratObj)
+  }
+
+  if (recalculateUCells) {
+    seuratObj <- RIRA::CalculateUCellScores(seuratObj, storeRanks = FALSE, assayName = 'RNA', forceRecalculate = TRUE, ncores = nCores)
+  }
+
   saveData(seuratObj, datasetId)
 
   # Cleanup

singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java

@@ -49,6 +49,18 @@ public Provider()
                     {{
                         put("checked", false);
                     }}, false),
+                    SeuratToolParameter.create("recalculateUCells", "Recalculate UCells", "If checked, RIRA::CalculateUCellScores will be re-run", "checkbox", new JSONObject()
+                    {{
+                        put("checked", true);
+                    }}, true),
+                    SeuratToolParameter.create("saveRepertoireStats", "Save TCR Repertoire Stats", "If checked, Rdiscvr::CalculateAndStoreTcrRepertoireStats will be run", "checkbox", new JSONObject()
+                    {{
+                        put("checked", true);
+                    }}, true),
+                    SeuratToolParameter.create("scoreActivation", "Score T Cell Activation", "If checked, RIRA::PredictTcellActivation will be run", "checkbox", new JSONObject()
+                    {{
+                        put("checked", true);
+                    }}, true),
                     SeuratToolParameter.create("keepOriginal", "Keep Copy of Original File", "If checked, the original file will be copied with the file extension '.bk'", "checkbox", new JSONObject()
                     {{
                         put("checked", false);