formatting fixed

RECETOX · Jan 6, 2025 · 1e29b19 · 1e29b19
1 parent 61e8751
commit 1e29b19
Showing 1 changed file with 52 additions and 52 deletions.
diff --git a/tools/scp/utils.R b/tools/scp/utils.R
@@ -5,72 +5,72 @@ 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
-  assay_data <- assay(qf[[assay_name]])
-  row_metadata <- as.data.frame(rowData(qf[[assay_name]]))
-  col_metadata <- as.data.frame(colData(qf))
+  # Function to export a single assay with metadata
+  export_assay_with_metadata <- function(qf, assay_name) {
+    # Extract assay data, row metadata, and col metadata
+    assay_data <- assay(qf[[assay_name]])
+    row_metadata <- as.data.frame(rowData(qf[[assay_name]]))
+    col_metadata <- as.data.frame(colData(qf))
 
-  # Combine row metadata with assay data
-  export_data <- cbind(RowNames = rownames(assay_data), row_metadata, as.data.frame(assay_data))
+    # Combine row metadata with assay data
+    export_data <- cbind(RowNames = rownames(assay_data), row_metadata, as.data.frame(assay_data))
 
-  # Save the table to a CSV file
-  output_file <- file.path("outputs", paste0(assay_name, "_export.csv"))
-  write.csv(export_data, output_file, row.names = FALSE)
-}
+    # Save the table to a CSV file
+    output_file <- file.path("outputs", paste0(assay_name, "_export.csv"))
+    write.csv(export_data, output_file, row.names = FALSE)
+  }
 
-# Export all assays
-export_all_assays <- function(qf) {
-  # Get the names of all assays
-  # assay_names <- names(assays(qf))
-  assay_names <- c("peptides", "peptides_norm", "peptides_log", "proteins", "proteins_norm", "proteins_imptd")
-  dir.create("outputs")
-  # Export each assay
-  for (assay_name in assay_names) {
-    export_assay_with_metadata(qf, assay_name)
+  # Export all assays
+  export_all_assays <- function(qf) {
+    # Get the names of all assays
+    # assay_names <- names(assays(qf))
+    assay_names <- c("peptides", "peptides_norm", "peptides_log", "proteins", "proteins_norm", "proteins_imptd")
+    dir.create("outputs")
+    # Export each assay
+    for (assay_name in assay_names) {
+      export_assay_with_metadata(qf, assay_name)
+    }
   }
-}
 
-# Plot the QC boxplots
+  # Plot the QC boxplots
 
-create_boxplots <- function(scp, i, is_log2, name) {
-  sce <- scp[[i]]
+  create_boxplots <- function(scp, i, is_log2, name) {
+    sce <- scp[[i]]
 
-  assay_data <- as.data.frame(assay(sce)) %>%
-    rownames_to_column("FeatureID")
+    assay_data <- as.data.frame(assay(sce)) %>%
+      rownames_to_column("FeatureID")
 
-  col_data <- as.data.frame(colData(scp)) %>%
-    rownames_to_column("SampleID") 
+    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"  
-    )
+    long_data <- assay_data %>%
+      pivot_longer(
+        cols = -FeatureID,  
+        names_to = "SampleID",  
+        values_to = "Value"  
+      )
 
-  long_data <- long_data %>%
-    left_join(col_data, by = "SampleID")
+    long_data <- long_data %>%
+      left_join(col_data, by = "SampleID")
 
-  if (is_log2 == TRUE){
-    long_data$Value <- log2(long_data$Value)
-  }
+    if (is_log2 == TRUE){
+      long_data$Value <- log2(long_data$Value)
+    }
 
-  long_data %>%
-    filter(Value != "NaN") %>%
-    ggplot(aes(x = runCol, y = Value, fill = SampleType))+
-    geom_boxplot() +
-    theme_bw() +
-    labs(title = name,
-         x = "Run",
-         y = "Log2 intensity") +
-    theme(axis.text.x = element_text(angle = 45, hjust=1))
-}
+    long_data %>%
+      filter(Value != "NaN") %>%
+      ggplot(aes(x = runCol, y = Value, fill = SampleType))+
+      geom_boxplot() +
+      theme_bw() +
+      labs(title = name,
+           x = "Run",
+           y = "Log2 intensity") +
+      theme(axis.text.x = element_text(angle = 45, hjust=1))
+  }
 
-# Heatmap
+  # Heatmap
 
-plot_heatmap <- function(scp, i){
+  plot_heatmap <- function(scp, i) {
     sce <- scp[[i]]
     heatmap_mat <- as.matrix(assay(sce))
     heatmap_mat[is.na(heatmap_mat)] <- 0