Allow most ADT processing steps to specify the assay name

Author: bbimber

singlecell/resources/chunks/CiteSeqDimReduxDist.R

@@ -2,8 +2,8 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    if (!('ADT' %in% names(seuratObj@assays))) {
-        print('ADT assay not present, skipping')
+    if (!(assayName %in% names(seuratObj@assays))) {
+        print(paste0(assayName, ' assay not present, skipping'))
     } else {
         tryCatch({
             seuratObj <- bindArgs(CellMembrane::CiteSeqDimRedux.Dist, seuratObj)()

singlecell/resources/chunks/CiteSeqDimReduxPca.R

@@ -2,8 +2,8 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    if (!('ADT' %in% names(seuratObj@assays))) {
-        print('ADT assay not present, skipping')
+    if (!(assayName %in% names(seuratObj@assays))) {
+        print(paste0(assayName, ' assay not present, skipping'))
     } else {
         seuratObj <- bindArgs(CellMembrane::CiteSeqDimRedux.PCA, seuratObj)()
     }

singlecell/resources/chunks/CiteSeqPlots.R

@@ -2,7 +2,6 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    assayName <- 'ADT'
     if (!(assayName %in% names(seuratObj@assays))) {
         print(paste0('Assay: ', assayName, ' not present, skipping'))
     } else {

singlecell/resources/chunks/CiteSeqWnn.R

@@ -3,8 +3,8 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
     tryCatch({
-        if (!('ADT' %in% names(seuratObj@assays))) {
-            print('ADT assay not present, skipping')
+        if (!(assayName %in% names(seuratObj@assays))) {
+            print(paste0(assayName, ' assay not present, skipping'))
         } else {
             seuratObj <- bindArgs(CellMembrane::RunSeuratWnn, seuratObj)()
         }

singlecell/resources/chunks/PlotAverageCiteSeqCounts.R

@@ -6,7 +6,7 @@ for (datasetId in names(seuratObjects)) {
     print('ADT assay not present, skipping')
   } else {
     tryCatch({
-      CellMembrane::PlotAverageAdtCounts(seuratObj, groupFields = fieldNames)
+      CellMembrane::PlotAverageAdtCounts(seuratObj, groupFields = fieldNames, assayName = assayName)
     }, error = function(e){
       print(paste0('Error running PlotAverageCiteSeqCounts for: ', datasetId))
       print(conditionMessage(e))

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

@@ -22,7 +22,10 @@ public Provider()
             super("CiteSeqDimReduxDist", "CiteSeq DimRedux (distance)", "CellMembrane/Seurat", "This will run DimRedux steps on the ADT data, based on euclidian distance.", Arrays.asList(
                     SeuratToolParameter.create("performClrNormalization", "Perform CLR Normalization", "If true, Seurat CLR normalization will be performed. Otherwise any pre-existing normalization is used.", "checkbox", new JSONObject(){{
                         put("checked", true);
-                    }}, true, "performClrNormalization", true)
+                    }}, true, "performClrNormalization", true),
+                    SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textbox", new JSONObject(){{
+
+                    }}, "ADT")
             ), null, null);
         }
 

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

@@ -30,8 +30,11 @@ public Provider()
                     SeuratToolParameter.create("adtBlacklist", "ADT Blacklist", "If provided, these ADTs will be excluded from scaling/PCA", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
-                    }}, null).delimiter(",")
-                    ), null, null);
+                    }}, null).delimiter(","),
+                    SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textbox", new JSONObject(){{
+
+                    }}, "ADT")
+            ), null, null);
         }
 
         @Override

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

@@ -1,9 +1,13 @@
 package org.labkey.singlecell.pipeline.singlecell;
 
+import org.json.JSONObject;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
 
+import java.util.Arrays;
+
 public class CiteSeqPlots extends AbstractCellMembraneStep
 {
     public CiteSeqPlots(PipelineContext ctx, CiteSeqPlots.Provider provider)
@@ -15,7 +19,11 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("CiteSeqPlots", "CiteSeq/ADT Plots", "CellMembrane/Seurat", "This will create FeaturePlots for all features in the ADT assay.", null, null, null);
+            super("CiteSeqPlots", "CiteSeq/ADT Plots", "CellMembrane/Seurat", "This will create FeaturePlots for all features in the ADT assay.", Arrays.asList(
+                    SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textbox", new JSONObject(){{
+
+                    }}, "ADT")
+            ), null, null);
         }
 
         @Override

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

@@ -26,7 +26,10 @@ public Provider()
                         put("allowBlank", false);
                         put("height", 150);
                         put("delimiter", ",");
-                    }}, "ClusterNames_0.2,ClusterNames_0.4,ClusterNames_0.6").delimiter(",")
+                    }}, "ClusterNames_0.2,ClusterNames_0.4,ClusterNames_0.6").delimiter(","),
+                    SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textbox", new JSONObject(){{
+
+                    }}, "ADT")
             ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }