attempt to fix vignette errors on Bioc build server

MarioniLab · Oct 16, 2024 · 66d18b5 · 66d18b5
1 parent 339c766
commit 66d18b5
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Showing 5 changed files with 38 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: miloR
 Type: Package
 Title: Differential neighbourhood abundance testing on a graph
-Version: 2.1.2
+Version: 2.1.3
 Authors@R:
     c(person("Mike", "Morgan", role=c("aut", "cre"), email="[email protected]",
      comment=c(ORCID="0000-0003-0757-0711")),
@@ -71,7 +71,7 @@ Suggests:
     curl,
     scRNAseq,
     graphics
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 NeedsCompilation: no
 Packaged: 2020-07-31 14:15:28 UTC; morgan02
 Collate: 

diff --git a/man/fitGLMM.Rd b/man/fitGLMM.Rd
diff --git a/man/plotNhoodGraph.Rd b/man/plotNhoodGraph.Rd
diff --git a/man/testNhoods.Rd b/man/testNhoods.Rd
diff --git a/vignettes/milo_glmm.Rmd b/vignettes/milo_glmm.Rmd
@@ -236,7 +236,7 @@ pbmc.milo <- buildNhoodGraph(pbmc.milo, overlap=25)
 
 # we need to subset the plotting results as it can't handle the NAs internally.
 plotUMAP(pbmc.milo, colour_by="adjmfc.time") + plotNhoodGraphDA(pbmc.milo, da_results[!is.na(da_results$logFC), ],
-                                                                subset.nhoods=!is.na(da_results$logFC), alpha=0.1) +
+                                                                alpha=0.1) +
   plot_layout(guides="auto" )
 ```