Include RIRA/Unknown in seurat description

Author: bbimber

singlecell/resources/chunks/RunRiraClassification.R

@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
+    seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix, maxAllowedUnknown = maxAllowedUnknown)
     seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
 
     seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)

singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java

@@ -948,6 +948,7 @@ public static String getOutputDescription(JSONObject jsonParams, Logger log, Fil
                 int totalDiscordant = 0;
                 int lowOrNegative = 0;
                 int totalDoublet = 0;
+                int totalUnknown = 0;
                 double totalSaturation = 0.0;
                 Set<String> subjectIds = new HashSet<>();
 
@@ -1073,6 +1074,10 @@ else if ("NotUsed".equals(val))
                                     cellsLackingCDR3++;
                                 }
                             }
+                            else if ("Unknown".equals(line[riraIdx]))
+                            {
+                                totalUnknown++;
+                            }
                         }
 
                         if (subjectIdIdx > 0)
@@ -1122,12 +1127,15 @@ else if ("NotUsed".equals(val))
                 }
                 else if (riraIdx == -1 || traIdx == -1)
                 {
-                    descriptions.add("TCR information not present");
+                    if (riraIdx != -1)
+                    {
+                        descriptions.add("TCR information not present");
+                    }
                 }
 
-                if (!subjectIds.isEmpty())
+                if (riraIdx != -1)
                 {
-                    descriptions.add("Distinct SubjectIds: " + subjectIds.size());
+                    descriptions.add("% RIRA/Unknown: " + pf.format((double)totalUnknown / (double)totalCells));
                 }
             }
             catch (IOException e)

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

@@ -27,6 +27,12 @@ public Provider()
                     SeuratToolParameter.create("retainProbabilityMatrix", "Retain Probability Matrix", "If true, the celltypist probability_matrix with per-class probabilities will be stored in meta.data", "checkbox", new JSONObject()
                     {{
                         put("checked", true);
+                    }}, true),
+                    SeuratToolParameter.create("maxAllowedUnknown", "Max Allowed Unknown", "If provided, ", "ldk-numberfield", new JSONObject()
+                    {{
+                        put("minValue", 0);
+                        put("maxValue", 1);
+                        put("decimalPrecision", 2);
                     }}, true)
             ), null, null);
         }