fixed formatting

tools/scp/utils.R

@@ -4,7 +4,6 @@ library(tidyr)
 library(tibble)
 
 # Export intermediate results 
-
 # Function to export a single assay with metadata
 export_assay_with_metadata <- function(qf, assay_name) {
     # Extract assay data, row metadata, and col metadata
@@ -33,27 +32,21 @@ export_all_assays <- function(qf) {
 # Plot the QC boxplots
 create_boxplots <- function(scp, i, is_log2, name) {
     sce <- scp[[i]]
-
     assay_data <- as.data.frame(assay(sce)) %>%
         rownames_to_column("FeatureID")
-
     col_data <- as.data.frame(colData(scp)) %>%
         rownames_to_column("SampleID") 
-
     long_data <- assay_data %>%
         pivot_longer(
-          cols = -FeatureID,  
-          names_to = "SampleID",  
-          values_to = "Value"  
+            cols = -FeatureID,  
+            names_to = "SampleID",  
+            values_to = "Value"  
         )
-
     long_data <- long_data %>%
         left_join(col_data, by = "SampleID")
-
     if (is_log2 == TRUE) {
         long_data$Value <- log2(long_data$Value)
     }
-
     long_data %>%
         filter(Value != "NaN") %>%
         ggplot(aes(x = runCol, y = Value, fill = SampleType)) +
@@ -63,7 +56,7 @@ create_boxplots <- function(scp, i, is_log2, name) {
             title = name,
             x = "Run",
             y = "Log2 intensity"
-            ) +
+        ) +
         theme(axis.text.x = element_text(angle = 45, hjust=1))
 }