Support min cells to keep param for TcrFilter

Author: bbimber

singlecell/resources/chunks/TcrFilter.R

@@ -26,7 +26,8 @@ for (datasetId in names(seuratObjects)) {
       return(length(intersect(values, cdr3ForLocus)) != 0)
     })
 
-    if (sum(matchingCells) == 0) {
+    if (sum(matchingCells) <= thresholdToKeep) {
+      print(paste0('Too few cells, skipping: ', datasetId))
       next
     }
 

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

@@ -21,12 +21,15 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("TcrFilter", "TCR-Based Filter", "CellMembrane/Seurat", "This will filter a seurat object based on TCR data.", Collections.singletonList(
+            super("TcrFilter", "TCR-Based Filter", "CellMembrane/Seurat", "This will filter a seurat object based on TCR data.", Arrays.asList(
                     SeuratToolParameter.create("cdr3s", "CDR3s To Keep", "A comma- or newline-delimited list of CDR3 sequences where locus prefixes the AA sequence (i.e. TRB:XXXXXX or TRA:YYYYYYY). Any cell matching any of these CDR3s will be kept. If that cell has multiple chains for a locus (i.e. 'CASSXXXXX,CASSYYYYY'), then only one of these needs to match for that cell to be kept. Also, all the input CDR3s should be single-chain (i.e. 'TRA:XXXXX', not 'TRA:XXXX,YYYY').", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
                         put("stripCharsRe", "/(^['\"]+)|(['\"]+$)/g");
-                    }}, null).delimiter(",")
+                    }}, null).delimiter(","),
+                    SeuratToolParameter.create("thresholdToKeep", "Min Cells To Keep", "If fewer than this many cells remain, the object will be discarded. This is primary present because seurat cannot easily accommodate objects with 1 cells", "ldk-integerfield", new JSONObject(){{
+                        put("minValue", 0);
+                    }}, 1)
             ), List.of("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }