Fix chris-mcginnis-ucsf#133

insectopalo · May 10, 2022 · 0710f5a · 0710f5a
1 parent 85f264b
commit 0710f5a
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Showing 4 changed files with 26 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -9,3 +9,7 @@ Description: DoubletFinder identifies doublets by generating artificial doublets
 License: CC-0
 Encoding: UTF-8
 LazyData: true
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
+RoxygenNote: 7.1.2
diff --git a/R/doubletFinder_v3.R b/R/doubletFinder_v3.R
@@ -113,14 +113,23 @@ doubletFinder_v3 <- function(seu, PCs, pN = 0.25, pK, nExp, reuse.pANN = FALSE,
     k <- round(nCells * pK)
     for (i in 1:n_real.cells) {
       neighbors <- order(dist.mat[, i])
+      cat("i: ", i, "\n")
+      cat(neighbors, "\n")
       neighbors <- neighbors[2:(k + 1)]
       pANN$pANN[i] <- length(which(neighbors > n_real.cells))/k
       if(!is.null(annotations)){
         for(ct in unique(annotations)){
-          neighbor_types[i,] <- 
-            table( doublet_types1[neighbors - n_real.cells] ) +
-            table( doublet_types2[neighbors - n_real.cells] )
-          neighbor_types[i,] <- neighbor_types[i,] / sum( neighbor_types[i,] )
+          cat(neighbors, "\n")
+          cat(n_real.cells, "\n")
+          neighbors_that_are_doublets = neighbors[neighbors>n_real.cells]
+          if(length(neighbors_that_are_doublets) > 0){
+            neighbor_types[i,] <-
+              table( doublet_types1[neighbors_that_are_doublets - n_real.cells] ) +
+              table( doublet_types2[neighbors_that_are_doublets - n_real.cells] )
+            neighbor_types[i,] <- neighbor_types[i,] / sum( neighbor_types[i,] )
+          } else {
+            neighbor_types[i,] <- NA
+          }
         }
       }
     }
@@ -133,7 +142,7 @@ doubletFinder_v3 <- function(seu, PCs, pN = 0.25, pK, nExp, reuse.pANN = FALSE,
     if(!is.null(annotations)){
       colnames(neighbor_types) = levels(doublet_types1)
       for(ct in levels(doublet_types1)){
-        seu@meta.data[, paste("DF.doublet.contributors",pN,pK,nExp,ct,sep="_")] <- neighbor_types[,ct] 
+        seu@meta.data[, paste("DF.doublet.contributors",pN,pK,nExp,ct,sep="_")] <- neighbor_types[,ct]
       }
     }
     return(seu)

diff --git a/man/doubletFinder_v3.Rd b/man/doubletFinder_v3.Rd
@@ -22,7 +22,7 @@ doubletFinder_V3(seu, PCs, pN = 0.25, pK, nExp, reuse.pANN = FALSE, sct = FALSE,
   }
   \item{sct}{ Logical representing whether SCTransform was used during original Seurat object pre-processing (default = FALSE).
   }
-  \item{annotations}{Optional character vector of cell type annotations. If provided, this function will keep track of the type of each artificial doublet and will yield guesses for what types were combined to form each doublet that is called. (default = NULL).
+  \item{annotations}{Optional character vector of cell type annotations. If provided, this function will keep track of the type of each artificial doublet and will yield guesses for constituent cell types. Specifically, it returns the proportion of different constituent cell types across all the artificial doublets that each cell is similar to. (default = NULL). For cells with no artificial doublet neighbors, the guesses will be NA.
   }
 }
 \details{

diff --git a/tests/testthat/test-doubletFinder_v3.R b/tests/testthat/test-doubletFinder_v3.R
@@ -19,7 +19,11 @@ test_that("doubletFinder_v3 works", {
     pbmc_small_dubs <- doubletFinder_v3(pbmc_small, PCs = 1:4, pN = 0.25, pK = 0.01, nExp = 5, reuse.pANN = FALSE, sct=FALSE,
                                         annotations = as.character(pbmc_small$RNA_snn_res.1))
   )
-  testthat::expect_length( pbmc_small_dubs$DF.doublet.contributors_0.25_0.01_5_0, 80 )
-  testthat::expect_length( pbmc_small_dubs$DF.doublet.contributors_0.25_0.01_5_1, 80 )
-  testthat::expect_length( pbmc_small_dubs$DF.doublet.contributors_0.25_0.01_5_2, 80 )
+  testthat::expect_output(
+    pbmc_small_dubs <- doubletFinder_v3(pbmc_small, PCs = 1:4, pN = 0.5, pK = 0.01, nExp = 5, reuse.pANN = FALSE, sct=FALSE,
+                                        annotations = as.character(pbmc_small$RNA_snn_res.1))
+  )
+  testthat::expect_length( pbmc_small_dubs$DF.doublet.contributors_0.5_0.01_5_0, 80 )
+  testthat::expect_length( pbmc_small_dubs$DF.doublet.contributors_0.5_0.01_5_1, 80 )
+  testthat::expect_length( pbmc_small_dubs$DF.doublet.contributors_0.5_0.01_5_2, 80 )
 })