view utils.r @ 0:cd2f3a280463 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit a0a1a3de5dd24b2aabe96ec3d6f89acdcf5e462b

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−# Export intermediate results
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−# Function to export a single assay with metadata
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−export_assay_with_metadata <- function(qf, assay_name) {
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−    # Extract assay data, row metadata, and col metadata
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−    assay_data <- SummarizedExperiment::assay(qf[[assay_name]])
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−    row_metadata <- as.data.frame(SummarizedExperiment::rowData(qf[[assay_name]]))
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−    col_metadata <- as.data.frame(SummarizedExperiment::colData(qf))
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−    # Combine row metadata with assay data
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−    export_data <- cbind(RowNames = rownames(assay_data), row_metadata, as.data.frame(assay_data))
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−    # Save the table to a CSV file
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−    output_file <- file.path("outputs", paste0(assay_name, "_export.txt"))
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−    write.table(export_data, output_file, row.names = FALSE, sep = "\t", quote = F)
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−}
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−
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−# Export all assays
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−export_all_assays <- function(qf) {
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−    # Get the names of all assays
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−    # assay_names <- names(assays(qf))
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−    assay_names <- c("peptides", "peptides_norm", "peptides_log", "proteins", "proteins_norm", "proteins_imptd")
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−    dir.create("outputs")
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−    # Export each assay
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−    for (assay_name in assay_names) {
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−        export_assay_with_metadata(qf, assay_name)
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−    }
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−}
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−
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−# Plot the QC boxplots
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−create_boxplots <- function(scp, i, is_log2, name) {
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−    sce <- scp[[i]]
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−    assay_data <- as.data.frame(SummarizedExperiment::assay(sce)) |>
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−        tibble::rownames_to_column("FeatureID")
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−    col_data <- as.data.frame(SummarizedExperiment::colData(scp)) |>
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−        tibble::rownames_to_column("SampleID")
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−    long_data <- assay_data |>
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−        tidyr::pivot_longer(
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−            cols = -FeatureID,
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−            names_to = "SampleID",
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−            values_to = "Value"
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−        )
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−    long_data <- long_data |>
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−        dplyr::left_join(col_data, by = "SampleID")
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−    if (is_log2 == TRUE) {
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−        long_data$Value <- log2(long_data$Value)
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−    }
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−    long_data |>
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−        dplyr::filter(Value != "NaN") |>
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−        ggplot2::ggplot(ggplot2::aes(x = runCol, y = Value, fill = SampleType)) +
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−        ggplot2::geom_boxplot() +
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−        ggplot2::theme_bw() +
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−        ggplot2::labs(
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−            title = name,
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−            x = "Run",
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−            y = "Log2 intensity"
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−        ) +
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−        ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1))
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−}
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−
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−# Heatmap
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−plot_heatmap <- function(scp, i) {
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−    sce <- scp[[i]]
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−    heatmap_mat <- as.matrix(SummarizedExperiment::assay(sce))
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−    heatmap_mat[is.na(heatmap_mat)] <- 0
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−    heatmap_bin <- ifelse(heatmap_mat > 0, 1, 0)
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−    colnames(heatmap_bin) <- gsub("Reporter.intensity.", "", colnames(heatmap_bin))
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−    heatmap(heatmap_bin, scale = "none", col = c("white", "black"), labRow = FALSE, margins = c(10, 5), cexCol = 0.5)
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−}