update assay names, correctly filter transcripts

wicky-dot · Nov 9, 2022 · 20c0b15 · 20c0b15
1 parent 425a0ab
commit 20c0b15
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/R/convenience.R b/R/convenience.R
@@ -197,9 +197,9 @@ LoadXenium <- function(data.dir, fov = 'fov', assay = 'Xenium') {
   )
 
   xenium.obj <- CreateSeuratObject(counts = data$matrix[["Gene Expression"]], assay = assay)
-  xenium.obj[["BLANK"]] <- CreateAssayObject(counts = data$matrix[["Blank Codeword"]])
-  xenium.obj[["DUMMY"]] <- CreateAssayObject(counts = data$matrix[["Negative Control Codeword"]])
-  xenium.obj[["ERCC"]] <- CreateAssayObject(counts = data$matrix[["Negative Control Probe"]])
+  xenium.obj[["BlankCodeword"]] <- CreateAssayObject(counts = data$matrix[["Blank Codeword"]])
+  xenium.obj[["ControlCodeword"]] <- CreateAssayObject(counts = data$matrix[["Negative Control Codeword"]])
+  xenium.obj[["ControlProbe"]] <- CreateAssayObject(counts = data$matrix[["Negative Control Probe"]])
 
   xenium.obj[[fov]] <- coords
   return(xenium.obj)

diff --git a/R/preprocessing.R b/R/preprocessing.R
@@ -2090,7 +2090,8 @@ ReadXenium <- function(
 
         # molecules
         if (has_dt) {
-          transcripts <- as.data.frame(data.table::fread(file.path(data.dir, "transcripts.csv.gz"))[qv >= mols.qv.threshold])
+          tx_dt <- as.data.frame(data.table::fread(file.path(data.dir, "transcripts.csv.gz")))
+          transcripts <- subset(tx_dt, qv >= mols.qv.threshold)
         } else {
           transcripts <- read.csv(file.path(data.dir, "transcripts.csv.gz"))
           transcripts <- subset(transcripts, qv >= mols.qv.threshold)