Rework default UCell sets

BimberLab · Feb 5, 2024 · f443c32 · f443c32
1 parent fb64839
commit f443c32
Show file tree

Hide file tree

Showing 2 changed files with 18 additions and 64 deletions.
diff --git a/R/GeneModules.R b/R/GeneModules.R
@@ -12,7 +12,7 @@
 #' @param storeRanks Passed directly to UCell::AddModuleScore_UCell. Increases object size but makes future calculations quicker.
 #' @param plotCor If true, a plot of correlations between the UCell score and each component gene will be shown
 #' @export
-CalculateUCellScores <- function(seuratObj, forceRecalculate = FALSE, seed = GetSeed(), ncores = 1, assayName = 'RNA', storeRanks = FALSE, plotCor = TRUE) {
+CalculateUCellScores <- function(seuratObj, forceRecalculate = FALSE, seed = GetSeed(), ncores = 1, assayName = 'RNA', storeRanks = TRUE, plotCor = TRUE) {
   toCalculate <- list(
     TandNK_Activation = GetGeneSet('TandNK_Activation.1'),
     TandNK_ActivationCore = GetGeneSet('TandNK_Activation.Core'),
@@ -22,7 +22,12 @@ CalculateUCellScores <- function(seuratObj, forceRecalculate = FALSE, seed = Get
     NaiveT = GetGeneSet('NaiveT'),
     Glycolysis = GetGeneSet('Glycolysis'),
     Interferon_Response = GetGeneSet('Interferon_Response'),
-    Interferon_Response_IFI6 = GetGeneSet('Interferon_Response_IFI6_correlated')
+    Interferon_Response_IFI6 = GetGeneSet('Interferon_Response_IFI6_correlated'),
+    Ribosomal = GetGeneSet('MMul10_Ribosomal'),
+    Mitochondrial = GetGeneSet('MMul10_Mitochondrial'),
+    EffectorCytokines = GetGeneSet('EffectorCytokines'),
+    ExhaustionOrInhibitory = GetGeneSet('ExhaustionOrInhibitory'),
+    MAIT_Markers = GetGeneSet('MAIT_Markers')
   )
 
   needsRecalc <- forceRecalculate || any(!paste0(names(toCalculate), '_UCell') %in% names(seuratObj@meta.data))
@@ -91,67 +96,14 @@ CalculateUCellScores <- function(seuratObj, forceRecalculate = FALSE, seed = Get
     print('No reductions calculated, cannot plot tSNE/UMAP')
   }
 
-  if (any(is.na(seuratObj[['TandNK_Activation_UCell']]))) {
-    print('Data has NAs, cannot make feature plot: TandNK_Activation_UCell')
-  } else {
-    if (hasReductions) {
-      print(Seurat::FeaturePlot(seuratObj, features = 'TandNK_Activation_UCell', min.cutoff = 'q02', max.cutoff = 'q98') + ggtitle('T Cell Activation Score'))
-    }
-  }
-
-  if (any(is.na(seuratObj[['TandNK_ActivationCore_UCell']]))) {
-    print('Data has NAs, cannot make feature plot: TandNK_ActivationCore_UCell')
-  } else {
-    if (hasReductions) {
-      print(Seurat::FeaturePlot(seuratObj, features = 'TandNK_ActivationCore_UCell', min.cutoff = 'q02', max.cutoff = 'q98') + ggtitle('T Cell Activation Score (Core Genes)'))
-    }
-  }
-
-  if (any(is.na(seuratObj[['Cytotoxicity_UCell']]))) {
-    print('Data has NAs, cannot make feature plot: Cytotoxicity_UCell')
-  } else {
-    if (hasReductions) {
-      print(Seurat::FeaturePlot(seuratObj, features = 'Cytotoxicity_UCell', min.cutoff = 'q05', max.cutoff = 'q95') + ggtitle('Cytotoxicity Score'))
-    }
-  }
-
-  if (any(is.na(seuratObj[['EffectorT_UCell']]))) {
-    print('Data has NAs, cannot make feature plot: EffectorT_UCell')
-  } else {
-    if (hasReductions) {
-      print(Seurat::FeaturePlot(seuratObj, features = 'EffectorT_UCell', min.cutoff = 'q05', max.cutoff = 'q95') + ggtitle('Effector T Score'))
-    }
-  }
-
-  if (any(is.na(seuratObj[['NaiveT_UCell']]))) {
-    print('Data has NAs, cannot make feature plot: NaiveT_UCell')
-  } else {
-    if (hasReductions) {
-      print(Seurat::FeaturePlot(seuratObj, features = 'NaiveT_UCell', min.cutoff = 'q05', max.cutoff = 'q95') + ggtitle('Naive T Score'))
-    }
-  }
-
-  if (any(is.na(seuratObj[['CentralMemT_UCell']]))) {
-    print('Data has NAs, cannot make feature plot: CentralMemT_UCell')
-  } else {
-    if (hasReductions) {
-      print(Seurat::FeaturePlot(seuratObj, features = 'CentralMemT_UCell', min.cutoff = 'q05', max.cutoff = 'q95') + ggtitle('Central Mem T Score'))
-    }
-  }
-
-  if (any(is.na(seuratObj[['Glycolysis_UCell']]))) {
-    print('Data has NAs, cannot make feature plot: Glycolysis_UCell')
-  } else {
-    if (hasReductions) {
-      print(Seurat::FeaturePlot(seuratObj, features = 'Glycolysis_UCell', min.cutoff = 'q05', max.cutoff = 'q95') + ggtitle('Glycolysis'))
-    }
-  }
-
-  if (any(is.na(seuratObj[['Interferon_Response_UCell']]))) {
-    print('Data has NAs, cannot make feature plot: Interferon_Response_UCell')
-  } else {
-    if (hasReductions) {
-      print(Seurat::FeaturePlot(seuratObj, features = 'Interferon_Response_UCell', min.cutoff = 'q05', max.cutoff = 'q95') + ggtitle('Interferon_Response'))
+  for (geneModule in names(toCalculate)) {
+    ucell <- paste0(geneModule, '_Cell')
+    if (any(is.na(seuratObj[[ucell]]))) {
+      print(paste0('Data has NAs, cannot make feature plot: ', ucell))
+    } else {
+      if (hasReductions) {
+        print(Seurat::FeaturePlot(seuratObj, features = ucell, min.cutoff = 'q02', max.cutoff = 'q98') + ggtitle(geneModule))
+      }
     }
   }
 

diff --git a/R/Phenotyping.R b/R/Phenotyping.R
@@ -91,7 +91,7 @@ PlotImmuneMarkers <- function(seuratObj, reductions = c('tsne', 'umap')) {
 	PlotMarkerSeries(seuratObj, reductions = reductions, features = c('HAVCR2'), 'Th1')
 
 	# ZBTB16 = PLZF
-	PlotMarkerSeries(seuratObj, reductions = reductions, features = c('KLRB1', 'CEPBD', 'NCR3', 'ZBTB16', 'RORC', 'SLC4A10', 'DPP4'), 'MAIT')
+	PlotMarkerSeries(seuratObj, reductions = reductions, features = GetGeneSet('MAIT_Markers'), 'MAIT')
 
 	# ZNF683 = HOBIT
 	# LOC100423131 = XCL1, ENSMMUG00000013779, Lymphotactin
@@ -329,6 +329,8 @@ GetGeneSet <- function(name) {
 
 .RegisterGeneSet('MMul10TcrConstantRegion', c('LOC710951', 'LOC114677140', 'LOC711031', 'LOC720538', 'LOC705095'))
 
+.RegisterGeneSet('MAIT_Markers', c('KLRB1', 'CEPBD', 'NCR3', 'ZBTB16', 'RORC', 'SLC4A10', 'DPP4'))
+
 # Dysfunction?
 # 'MT1A', 'MT2A', 'MT1M'
 .RegisterGeneSet('MMul10TcrGenes', c('LOC703029','LOC696306','LOC106999340','LOC106996262','LOC106999345','LOC106997707','LOC106997706','LOC710149','LOC700771','LOC699427','LOC711871','LOC709081','LOC698785','LOC114677052','LOC114676933','LOC106999353','LOC106999351','LOC106999350','LOC106999349','LOC106999348','LOC106999347','LOC106999346','LOC106999343','LOC106999341','LOC106999339','LOC106999337','LOC106999336','LOC106999335','LOC106999312','LOC106997705','LOC106997704','LOC106997703','LOC106997702','LOC106997697','LOC106997453','LOC106997452','LOC106997451','LOC106995765','LOC106992460','LOC106992446','LOC106992434','LOC106992433','LOC720456','LOC716949','LOC716866','LOC711537','LOC711386','LOC711194','LOC711141','LOC711066','LOC710821','LOC710627','LOC710455','LOC710361','LOC710183','LOC710093','LOC709531','LOC708581','LOC708328','LOC704883','LOC703153','LOC702904','LOC702550','LOC702113','LOC701992','LOC701875','LOC701745','LOC701395','LOC701262','LOC701152','LOC700224','LOC700154','LOC700105','LOC699912','LOC699790','LOC699543','LOC699298','LOC699162','LOC698913','LOC698543','LOC698289','LOC698161','LOC697792','LOC697466','LOC697234','LOC697054','LOC696752','LOC696684','LOC696557','LOC696075','LOC695943','LOC114679533','LOC114679531','LOC114677139','LOC114677137','LOC114677136','LOC114677055','LOC114677054','LOC114677050','LOC114677049','LOC114677047','LOC114675766'))