use sample_name as the colnames of resulting SummarizedExperiment object

Nesvilab · Nov 28, 2024 · d0d1a65 · d0d1a65
1 parent a1260ca
commit d0d1a65
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/R/io.R b/R/io.R
@@ -486,7 +486,8 @@ make_se_customized <- function(proteins_unique, columns, expdesign, log2transfor
     )
   }
 
-  colnames(raw)[matched] <- expdesign$label
+  rownames(expdesign) <- expdesign$sample_name
+  colnames(raw)[matched] <- expdesign$sample_name
   raw <- raw[, !is.na(colnames(raw))][rownames(expdesign)]
 
   # Select the rowData

diff --git a/R/pca.R b/R/pca.R
@@ -1,6 +1,6 @@
 #' @export
 plot_pca <- function(dep, x = 1, y = 2, indicate = c("condition", "replicate"),
-                     label = FALSE, n = 500, point_size = 8, label_size = 3, plot = TRUE, ID_col = "label", exp = NULL, scale=F, interactive = F) {
+                     label = FALSE, n = 500, point_size = 8, label_size = 3, plot = TRUE, ID_col = "sample_name", exp = NULL, scale=F, interactive = F) {
   if (is.null(exp)) {
     exp <- metadata(dep)$exp
   }