From 1bd8483501cababca1bf07e1fc1d4cd4302e6e2f Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Tue, 12 Dec 2023 16:44:28 +0100
Subject: [PATCH] Initialize objects with colnames and add check to
 binAcrossPixels

---
 NEWS                | 2 ++
 R/binAcrossPixels.R | 8 ++++++--
 R/read_cpout.R      | 3 +++
 R/read_steinbock.R  | 3 +++
 4 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/NEWS b/NEWS
index 8dfc183..3a36587 100644
--- a/NEWS
+++ b/NEWS
@@ -216,4 +216,6 @@ Changes in version 1.7.8 (2023-10-19)
 Changes in version 1.9.1 (2023-11-20)
 
 + Switched from aes_ to .data
++ Initialise SPE and SCE objects with colnames
++ Additional test within binAcrossPixels
 
diff --git a/R/binAcrossPixels.R b/R/binAcrossPixels.R
index 722f278..5e3eb3a 100644
--- a/R/binAcrossPixels.R
+++ b/R/binAcrossPixels.R
@@ -54,8 +54,12 @@ binAcrossPixels <- function(object,
         stop("'statistic' must be 'sum', 'mean' or 'median'.")
     }
     
-    cur_split <- split(object[[spot_id]], f = object[[spot_id]])
-    cur_split <- lapply(cur_split, function(x){ceiling(seq_along(x)/bin_size)})
+    cur_split_tmp <- split(object[[spot_id]], f = object[[spot_id]])
+    cur_split <- lapply(cur_split_tmp, function(x){ceiling(seq_along(x)/bin_size)})
+    
+    if (!isTRUE(all.equal(unlist(cur_split_tmp), object[[spot_id]]))) {
+        stop("Spot IDs of pixels within 'object' are not ordered alphabetically.")
+    }
     
     cur_df <- DataFrame(spot_id = object[[spot_id]],
                         bin = unlist(cur_split))
diff --git a/R/read_cpout.R b/R/read_cpout.R
index 373530f..87c0118 100644
--- a/R/read_cpout.R
+++ b/R/read_cpout.R
@@ -171,5 +171,8 @@ read_cpout <- function(path,
     
     object <- .add_panel(object, path, panel_file, extract_metal_from)
     
+    # Add colnames
+    colnames(object) <- paste0(object$sample_id, "_", object$ObjectNumber)
+    
     return(object)
 }
diff --git a/R/read_steinbock.R b/R/read_steinbock.R
index 178e153..42337ad 100644
--- a/R/read_steinbock.R
+++ b/R/read_steinbock.R
@@ -161,5 +161,8 @@ read_steinbock <- function(path,
     # Add panel data
     object <- .add_panel(object, path, panel_file, extract_names_from)
     
+    # Add colnames
+    colnames(object) <- paste0(object$sample_id, "_", object$ObjectNumber)
+    
     return(object)
 }