Improve seurat subsetting (#108)

BimberLab · Nov 15, 2023 · 954495b · 954495b
1 parent 652ac32
commit 954495b
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/R/CellTypist.R b/R/CellTypist.R
@@ -530,7 +530,7 @@ FilterDisallowedClasses <- function(seuratObj, sourceField = 'RIRA_Immune_v2.maj
         }
       }
 
-      x <- colnames(seuratObj)[seuratObj[[sourceField]] == cls & seuratObj[[ucell]] > ucellCutoff]
+      x <- colnames(seuratObj)[seuratObj@meta.data[[sourceField]] == cls & seuratObj@meta.data[[ucell]] > ucellCutoff]
       if (length(x) > 0) {
         toDrop <- rbind(toDrop, data.frame(cellbarcode = x, reason = ucell))
       }

diff --git a/R/ComponentScores.R b/R/ComponentScores.R
@@ -39,7 +39,7 @@ ScoreUsingSavedComponent <- function(seuratObj, componentOrName, fieldName) {
   seuratObj <- Seurat::AddMetaData(seuratObj, cellScores, col.name = fieldName)
 
   suppressMessages(print(FeaturePlot(seuratObj, features = fieldName, order = T) & ggplot2::scale_colour_gradientn(colours = c("navy", "dodgerblue", "gold", "red"))))
-  graphics::hist(seuratObj[[fieldName]][,1], breaks = 300, main = fieldName)
+  graphics::hist(seuratObj@meta.data[[fieldName]], breaks = 300, main = fieldName)
 
   return(seuratObj)
 }