Initialize objects with colnames and add check to binAcrossPixels

BodenmillerGroup · Dec 12, 2023 · 1bd8483 · 1bd8483
1 parent 1dc534e
commit 1bd8483
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Showing 4 changed files with 14 additions and 2 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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)
 }