Improve default nimble append

bimberlabinternal · Jan 31, 2025 · b61a726 · b61a726
1 parent 75e956d
commit b61a726
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diff --git a/R/NimbleAPI.R b/R/NimbleAPI.R
@@ -460,6 +460,8 @@ PerformDefaultNimbleAppend <- function(seuratObj, isotypeFilterThreshold = 0.1,
 }
 
 .GroupMhcData <- function(seuratObj, targetAssay, sourceAssay = 'MHC', prefix = 'Mamu-', assayForLibrarySize = 'RNA') {
+  seuratObj <- .AssignLocusToMhcFeatures(seuratObj, sourceAssayName = sourceAssay)
+
   ad <- Seurat::GetAssay(seuratObj, assay = sourceAssay)
   groupedMHC <- .RegroupCountMatrix(Seurat::GetAssayData(seuratObj, assay = sourceAssay, layer = 'counts'), featureTransform = function(x){
     return(ad@meta.features$locus[rownames(ad) == x])

diff --git a/R/NimbleAppend.R b/R/NimbleAppend.R
@@ -111,7 +111,7 @@ AppendNimbleCounts <- function(seuratObject, nimbleFile, targetAssayName, maxAmb
 
       x <- sort(table(x), decreasing = T)
       x <- data.frame(Feature = names(x), Total = as.numeric(unname(x)))
-      x$Fraction <- x$Total / totalUMI
+      x$Total <- paste0(x$Total, ' (', scales::percent(x$Total / totalUMI, accuracy = 0.001), ')')
       print(x)
       df <- df[!ambigFeatRows, , drop = F]