From e1deaa8e315205cdd86f5085b456637e706f934f Mon Sep 17 00:00:00 2001
From: maxim-h <maksim.holmatov@gmail.com>
Date: Wed, 20 Mar 2024 17:23:51 +0100
Subject: [PATCH] Add warning if layer is absent from assay

This is meant to help diagnose issues when assay doesn't have desired layer.
For example see satijalab/seurat#8658 and discussion in satijalab/seurat#8659.

The warning message might not be the prettiest, but I didn't want to go through `Layer.Seurat` method to get the assay name.
---
 R/assay.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/R/assay.R b/R/assay.R
index c96de65f..67a75cf4 100644
--- a/R/assay.R
+++ b/R/assay.R
@@ -697,6 +697,11 @@ Layers.Assay <- function(object, search = NA, ...) {
   if (!is_na(x = search)) {
     layers <- intersect(x = search, y = layers)
     if (length(x = layers) == 0) {
+      warning(
+        "Layer ", search, " isn't present in the assay ", deparse(substitute(object)), ". Returning NULL.",
+        call. = FALSE,
+        immediate. = TRUE
+      )
       return(NULL)
     }
   }