From 3f825b946f21f2b2ccd2331aaf1672ce6615b778 Mon Sep 17 00:00:00 2001
From: missaroa <missaroa@gene.com>
Date: Thu, 4 Apr 2024 17:54:21 -0700
Subject: [PATCH] add simpler milo check for plotting functions

---
 DESCRIPTION            |  2 +-
 R/plotting_functions.R |  2 +-
 R/utils.R              | 23 +++++++++++++++++++++++
 3 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index bb5c257..0f2d923 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -8,7 +8,7 @@ Description: Sensitive DE testing using neighbourhoods instead of discrete clust
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Imports: 
     dplyr,
     ggplot2,
diff --git a/R/plotting_functions.R b/R/plotting_functions.R
index cc67ddf..ace0e41 100644
--- a/R/plotting_functions.R
+++ b/R/plotting_functions.R
@@ -67,7 +67,7 @@ plot_milo_by_single_metric = function(x, nhood_stat, colour_by = "logFC" , signi
 
   # checks
   out = .check_argument_correct(x, .check_sce, "Check x - something is wrong (gene names unique? reducedDim.name is not present?)") &
-    .check_sce_milo(x) &
+    .check_sce_milo_wo_graph(x) &
     .check_argument_correct(order_direction, .check_boolean, "Check order_direction - should be either TRUE or FALSE") &
     .check_reducedDim_in_sce(x , layout) & .check_nhood_stat(nhood_stat , x)
 
diff --git a/R/utils.R b/R/utils.R
index 5207446..78b3e5d 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -28,6 +28,29 @@
   }
 }
 
+# sce-milo check wo/ calculation of the length of graph: that is used in plotting functions
+#' @importFrom miloR Milo nhoods graph graph<- nhoods<- nhoodIndex<- buildNhoodGraph
+#' @importFrom methods is
+.check_sce_milo_wo_graph = function(x){
+  if (!is(x , "Milo")){
+    stop("x should be a Milo object. Please run `assign_neighbourhoods` first.")
+    return(FALSE)
+  } else if (sum(sum(nhoods(x))) == 0){
+    stop("x should have calculated nhoods. Please run 'assign_neighbourhoods' first.")
+    return(FALSE)
+  } else if ( nrow(nhoods(x)) == 1 & ncol(nhoods(x)) == 1 ){
+    stop("x should contain non-trivial nhoods. Please run `assign_neighbourhoods` first.")
+    return(FALSE)
+  } else if (isEmpty(nhoodIndex(x))){
+    stop("x should have calculated nhoodIndex. Please run 'assign_neighbourhoods' first.")
+    return(FALSE)
+  } else {
+    return(TRUE)
+  }
+}
+
+
+
 # sce check: that is used in add_embedding
 #' @importFrom SingleCellExperiment reducedDimNames
 #' @importFrom SummarizedExperiment assays<- assays