allow DESeq, DataFrame objs as annot

mschubert · Feb 12, 2025 · ed93cfc · ed93cfc
1 parent ab2eb1e
commit ed93cfc
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/plot/pca.r b/plot/pca.r
@@ -33,6 +33,10 @@ pca.prcomp = function(obj, aes, annot=NULL, repel=TRUE,
         aes$x = quote(PC1)
     if (!"y" %in% names(aes))
         aes$y = quote(PC2)
+    if (inherits(annot, "DESeqDataSet") || inherits(annot, "DESeqTransform"))
+        annot = SummarizedExperiment::colData(annot)
+    if (inherits(annot, "DataFrame"))
+        annot = as.data.frame(annot)
 
     # adapted: https://stackoverflow.com/questions/6578355/plotting-pca-biplot-with-ggplot2
     data = as.data.frame(cbind(annot, obj$x))