Fix bug in splatSimPathDE()

DE factors are now adjusted for the originating path
Oshlack · Oct 11, 2023 · 3ee127b · 3ee127b
1 parent e253676
commit 3ee127b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.25.0
-Date: 2023-04-26
+Version: 1.25.1
+Date: 2023-10-11
 Authors@R:
     c(person("Luke", "Zappia", role = c("aut", "cre"),
       email = "luke@lazappi.id.au",

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,12 @@
 ## DEVELOPMENT VERSION
 
+## Version 1.25.1 (2023-10-11)
+
+* Fix a bug in splatSimPathDE() where DE factors were not adjusted based on the
+  path origin (path.from parameter). This affected paths where the path origin
+  was not the simulation origin (path.from != 0), particularly when the path DE
+  was minimal.
+
 ## Version 1.25.0 (2023-04-26)
 
 Bioconductor 3.18 devel

diff --git a/R/splat-simulate.R b/R/splat-simulate.R
@@ -463,13 +463,15 @@ splatSimPathDE <- function(sim, params) {
     for (path in path.order) {
         from <- path.from[path]
         if (from == 0) {
-            means.gene <- rowData(sim)$GeneMean
+            de.facs.from <- rep(1, nGenes)
         } else {
-            means.gene <- rowData(sim)[[paste0("GeneMeanPath", from)]]
+            de.facs.from <- rowData(sim)[[paste0("DEFacPath", from)]]
         }
-        de.facs <- getLNormFactors(nGenes, de.prob[path], de.downProb[path],
-                                   de.facLoc[path], de.facScale[path])
-        path.means.gene <- means.gene * de.facs
+        de.facs.local <- getLNormFactors(nGenes, de.prob[path],
+                                         de.downProb[path], de.facLoc[path],
+                                         de.facScale[path])
+        de.facs <- de.facs.local * de.facs.from
+        rowData(sim)[[paste0("LocalDEFacPath", path)]] <- de.facs.local
         rowData(sim)[[paste0("DEFacPath", path)]] <- de.facs
     }
 

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -3,7 +3,13 @@
 
 \section{Version 1.26.0, Bioconductor 3.18 Release (2023-10-25)}{
   \itemize{
-    No changes since the previous release
+    \item{
+      Fixed a bug in \code{splatSimPathDE()} where DE factors were not adjusted
+      based on the path origin (\code{path.from} parameter). This affected paths
+      where the path origin was not the simulation origin (i.e.
+      \code{path.from != 0}), particularly when the path DE was minimal.
+      With this fix paths should no longer drift towards the origin.
+    }
   }
 }