From 77c95d5d3aa5d59d522654b5a7aa5a2102ade262 Mon Sep 17 00:00:00 2001
From: tfguinan <59532990+tfguinan@users.noreply.github.com>
Date: Thu, 18 Jan 2024 16:18:54 +1100
Subject: [PATCH 1/2] Update project_query.R GetAssayData() inline with Seurat
 v5

---
 R/project_query.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/project_query.R b/R/project_query.R
index 4c8ab89..aee5edc 100644
--- a/R/project_query.R
+++ b/R/project_query.R
@@ -84,7 +84,7 @@ if(alignment){
   
   
   
-  new_data <- GetAssayData(new, "data")[shared_features,]
+  new_data <- GetAssayData(new, layer="data")[shared_features,]
   means <- spmodel@scaling$means
   stdevs  <- spmodel@scaling$stdevs
   new_data <- Matrix::t(new_data)

From 9f407b7436f40d44224a5976a94cc6815c6e837f Mon Sep 17 00:00:00 2001
From: tfguinan <59532990+tfguinan@users.noreply.github.com>
Date: Thu, 18 Jan 2024 16:22:09 +1100
Subject: [PATCH 2/2] Update project_query.R

Not sure why the newline did something
---
 R/project_query.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/project_query.R b/R/project_query.R
index aee5edc..73002e1 100644
--- a/R/project_query.R
+++ b/R/project_query.R
@@ -47,7 +47,7 @@ if("scpred" %in% names(new@reductions)){
   if(recompute_alignment){
     alignment <- TRUE
     cat(crayon::yellow(cli::symbol$figure_dash, "Data has already been aligned to a reference.\n"), sep = "")
-    cat(crayon::yellow(cli::symbol$sup_plus, "Skip data alignment using `recompute.alignment = FALSE`.\n"),  sep = "")
+    cat(crayon::yellow(cli::symbol$sup_plus, "Skip data alignment using 'recompute.alignment = FALSE'.\n"),  sep = "")
       
   } 
   else {