Updated runBarcodeRanks() to match output from new DropletUtils update

compbiomed · Feb 20, 2025 · b4c3146 · b4c3146
1 parent 974ed6b
commit b4c3146
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Showing 2 changed files with 12 additions and 11 deletions.
diff --git a/R/dropletUtils_barcodeRank.R b/R/dropletUtils_barcodeRank.R
@@ -9,20 +9,20 @@
                                        fit.bounds = fit.bounds,
                                        df = df)
 
-  knee.ix <- as.integer(output@listData$total >= 
+  knee.ix <- as.integer(output$total >= 
                           S4Vectors::metadata(output)$knee)
-  inflection.ix <- as.integer(output@listData$total >= 
+  inflection.ix <- as.integer(output$total >= 
                                 S4Vectors::metadata(output)$inflection)
+
   rank.ix <- as.integer(output$rank)
   total.ix <- as.integer(output$total)
-  fitted.ix <- as.integer(output$fitted)
 
-  result <- cbind(knee.ix, inflection.ix, rank.ix, total.ix, fitted.ix)
+  result <- cbind(knee.ix, inflection.ix, rank.ix, total.ix)
   colnames(result) <- c("dropletUtils_barcodeRank_knee",
                         "dropletUtils_barcodeRank_inflection",
                         "dropletUtils_barcodeRank_rank",
-                        "dropletUtils_barcodeRank_total",
-                        "dropletUtils_barcodeRank_fitted")
+                        "dropletUtils_barcodeRank_total")
+
   result.list <- list(result,
                       S4Vectors::metadata(output)$knee,
                       S4Vectors::metadata(output)$inflection)
@@ -117,8 +117,7 @@ runBarcodeRankDrops <- function(inSCE,
                         "dropletUtils_barcodeRank_inflection")]
 
     metaCols <- c("dropletUtils_barcodeRank_rank", 
-                  "dropletUtils_barcodeRank_total",
-                  "dropletUtils_barcodeRank_fitted")
+                  "dropletUtils_barcodeRank_total")
     metaOutput[, metaCols] <- result.matrix[, metaCols]
     metaOutput[,"dropletUtils_barcodeRank_knee"] <- rep(result$knee,
                                                         sum(sceSampleInd))

diff --git a/tests/testthat/test-dropletUtils.R b/tests/testthat/test-dropletUtils.R
@@ -5,8 +5,10 @@ context("Testing dropletUtils algorithms")
 data(scExample, package = "singleCellTK")
 
 test_that(desc = "Testing runBarcodeRankDrops", {
-        sceres <- runBarcodeRankDrops(inSCE = sce)
-        expect_equal(length(colData(sceres)$dropletUtils_BarcodeRank_Inflection),ncol(sce))
-        expect_equal(class(colData(sceres)$dropletUtils_BarcodeRank_Inflection), "integer")
+        sce <- runBarcodeRankDrops(inSCE = sce)
+        expect_equal(length(colData(sce)$dropletUtils_BarcodeRank_Inflection),ncol(sce))
+        expect_equal(class(colData(sce)$dropletUtils_BarcodeRank_Inflection), "integer")
+        gg <- plotBarcodeRankDropsResults(sce)
+        expect_is(gg$scatterBarcodeRank, "ggplot")
 })