--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.r	Wed Jan 22 07:44:00 2025 +0000
@@ -0,0 +1,66 @@
+# 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 <- SummarizedExperiment::assay(qf[[assay_name]])
+    row_metadata <- as.data.frame(SummarizedExperiment::rowData(qf[[assay_name]]))
+    col_metadata <- as.data.frame(SummarizedExperiment::colData(qf))
+    # 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.txt"))
+    write.table(export_data, output_file, row.names = FALSE, sep = "\t", quote = F)
+}
+
+# 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
+create_boxplots <- function(scp, i, is_log2, name) {
+    sce <- scp[[i]]
+    assay_data <- as.data.frame(SummarizedExperiment::assay(sce)) |>
+        tibble::rownames_to_column("FeatureID")
+    col_data <- as.data.frame(SummarizedExperiment::colData(scp)) |>
+        tibble::rownames_to_column("SampleID")
+    long_data <- assay_data |>
+        tidyr::pivot_longer(
+            cols = -FeatureID,
+            names_to = "SampleID",
+            values_to = "Value"
+        )
+    long_data <- long_data |>
+        dplyr::left_join(col_data, by = "SampleID")
+    if (is_log2 == TRUE) {
+        long_data$Value <- log2(long_data$Value)
+    }
+    long_data |>
+        dplyr::filter(Value != "NaN") |>
+        ggplot2::ggplot(ggplot2::aes(x = runCol, y = Value, fill = SampleType)) +
+        ggplot2::geom_boxplot() +
+        ggplot2::theme_bw() +
+        ggplot2::labs(
+            title = name,
+            x = "Run",
+            y = "Log2 intensity"
+        ) +
+        ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1))
+}
+
+# Heatmap
+plot_heatmap <- function(scp, i) {
+    sce <- scp[[i]]
+    heatmap_mat <- as.matrix(SummarizedExperiment::assay(sce))
+    heatmap_mat[is.na(heatmap_mat)] <- 0
+    heatmap_bin <- ifelse(heatmap_mat > 0, 1, 0)
+    colnames(heatmap_bin) <- gsub("Reporter.intensity.", "", colnames(heatmap_bin))
+    heatmap(heatmap_bin, scale = "none", col = c("white", "black"), labRow = FALSE, margins = c(10, 5), cexCol = 0.5)
+}