@platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software 1.7.0

package/.turbo/turbo-build.log

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+ WARN  Issue while reading "/home/runner/work/differential-clonotype-abundance/differential-clonotype-abundance/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
+
+> @platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software@1.7.0 build /home/runner/work/differential-clonotype-abundance/differential-clonotype-abundance/software
+> pl-pkg build
+
+info: Rendering entrypoint descriptors...
+info: Writing entrypoint descriptor to '/home/runner/work/differential-clonotype-abundance/differential-clonotype-abundance/software/dist/tengo/software/main.sw.json'
+info: Building software package 'main' for platform 'linux-x64'...
+info:   packing software into a package
+info:     generating cross-platform package
+info:   software package was written to '/home/runner/work/differential-clonotype-abundance/differential-clonotype-abundance/software/pkg-platforma-open-milaboratories.run-diff-clonotype-abundance-deseq2-r.software-main-1.7.0.tgz'

package/CHANGELOG.md

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+# @platforma-open/milaboratories.run-deseq2-r.software
+
+## 1.7.0
+
+### Minor Changes
+
+- 2086193: Fix software naming
+
+## 1.6.0
+
+### Minor Changes
+
+- 83b4ffc: Package updates
+- e2f5931: First MVB

package/dist/tengo/software/main.sw.json

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+{"name":"@platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software:main","binary":{"type":"R","registry":"platforma-open","package":"platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software/main/1.7.0.tgz","cmd":["Rscript","{pkg}/run_onlyDESeq2.R"],"envVars":[],"runEnv":{"name":"@platforma-open/milaboratories.runenv-r-differential-expression:main","type":"R","registry":"platforma-open","package":"platforma-open/milaboratories.runenv-r-differential-expression/main/1.0.7-{os}-{arch}.tgz","binDir":"bin"},"toolset":"renv","dependencies":{}}}

package/package.json

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+{
+  "name": "@platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software",
+  "version": "1.7.0",
+  "type": "module",
+  "description": "Block Software: Run DESeq2 with R",
+  "block-software": {
+    "entrypoints": {
+      "main": {
+        "binary": {
+          "artifact": {
+            "type": "R",
+            "registry": "platforma-open",
+            "environment": "@platforma-open/milaboratories.runenv-r-differential-expression:main",
+            "root": "./src"
+          },
+          "cmd": [
+            "Rscript",
+            "{pkg}/run_onlyDESeq2.R"
+          ]
+        }
+      }
+    }
+  },
+  "devDependencies": {
+    "@platforma-open/milaboratories.runenv-r-differential-expression": "^1.0.6",
+    "@platforma-sdk/package-builder": "^2.15.6"
+  },
+  "scripts": {
+    "build": "pl-pkg build",
+    "do-pack": "rm -f *.tgz && pl-pkg build && pnpm pack && mv platforma-open*.tgz package.tgz",
+    "changeset": "changeset",
+    "version-packages": "changeset version"
+  }
+}

package/src/run_onlyDESeq2.R

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+#!/usr/bin/env Rscript
+
+# Load libraries
+suppressMessages(library("optparse"))
+suppressMessages(library("tidyr"))
+suppressMessages(library("dplyr"))
+suppressMessages(library("DESeq2"))
+
+
+# DESeq2 script using above declared functions
+option_list <- list(
+  make_option(c("-c", "--count_matrix"), type = "character", default = NULL,
+              help = "Path to count matrix CSV file", metavar = "character"),
+  make_option(c("-m", "--metadata"), type = "character", default = NULL,
+              help = "Path to metadata CSV file", metavar = "character"),
+  make_option(c("-t", "--contrast_factor"), type = "character", default = NULL,
+              help = "Column name in metadata for the contrast",
+              metavar = "character"),
+  make_option(c("-n", "--numerator"), type = "character", default = NULL,
+              help = "Numerator level for contrast factor",
+              metavar = "character"),
+  make_option(c("-d", "--denominator"), type = "character", default = NULL,
+              help = "Denominator level for contrast factor",
+              metavar = "character"),
+  make_option(c("-o", "--output"), type = "character",
+              default = "deseq2_results.csv",
+              help = "Output CSV file for results", metavar = "character"),
+  make_option(c("-f", "--fc_threshold"), type = "double", default = 1,
+              help = "Adjusted p-value threshold for significance"),
+  make_option(c("-p", "--p_threshold"), type = "double", default = 0.05,
+              help = "Adjusted p-value threshold for significance"),
+  make_option(c("-v", "--values_column"), type = "character", 
+              default = "Number of UMIs",
+              help = "Name of column containing counts"),
+  make_option(c("-i", "--IDs_column"), type = "character",
+              default = "Clonotype key",
+              help = "Name of column containing gene/clonotype IDs"),
+  make_option(c("-x", "--min_counts"), type = "double", default = 5,
+              help = "minimum number of counts in fraction of samples defined by fraction_for_filter"),
+  make_option(c("-y", "--fraction_for_filter"), type = "double", default = 0.9,
+              help = "Fraction of samples that should have more than X min_counts to be accepted in analysis")
+)
+
+opt_parser <- OptionParser(option_list = option_list)
+opt <- parse_args(opt_parser)
+
+if (is.null(opt$count_matrix) || is.null(opt$metadata) || is.null(opt$contrast_factor) || is.null(opt$numerator) || is.null(opt$denominator)) {
+  stop("Missing required arguments")
+}
+
+# Load count matrix and covariates metadata
+count_long <- read.csv(opt$count_matrix, check.names = FALSE)
+metadata <- read.csv(opt$metadata, row.names = 1, check.names = FALSE)
+
+# Rename some input variables
+values_col <- opt$values_column
+ids_col <- opt$IDs_column
+min_counts <- opt$min_counts
+filter_fraction <- opt$fraction_for_filter
+
+# Validate contrast factor
+if (!opt$contrast_factor %in% colnames(metadata)) {
+  stop("Contrast factor column not found in metadata")
+}
+if (!(opt$numerator %in% metadata[[opt$contrast_factor]])) {
+  stop("Numerator not found in contrast factor column")
+}
+if (!(opt$denominator %in% metadata[[opt$contrast_factor]])) {
+  stop("Denominator not found in contrast factor column")
+}
+
+colnames(metadata) <- make.names(colnames(metadata))
+
+# Transform long format to wide format
+count_matrix <- count_long %>%
+  pivot_wider(names_from = Sample, values_from = values_col) %>%
+  as.data.frame()
+
+# Set Id columns as row name and remove it
+rownames(count_matrix) <- count_matrix[, ids_col]
+count_matrix <- count_matrix[, -1]
+
+# Convert NA values to zero
+count_matrix[is.na(count_matrix)] <- 0
+
+# Apply filter by low counts (at least filter by values in one sample)
+min_samples <- max(floor(ncol(count_matrix) * filter_fraction), 1)
+count_matrix <- count_matrix[rowSums(count_matrix >= min_counts) >= min_samples, ]
+
+# Prepare DESeq2 dataset
+dds <- DESeqDataSetFromMatrix(
+  countData = count_matrix,
+  colData = metadata,
+  design = as.formula(paste("~", paste(colnames(metadata), collapse = " + ")))
+)
+dds <- DESeq(dds, fitType = "local")
+
+
+# Extract topTable
+res <- results(dds, contrast = c(make.names(opt$contrast_factor), opt$numerator, opt$denominator))
+res_df <- as.data.frame(res)
+
+# Tidy table
+res_df[ids_col] <- rownames(res_df)
+res_df$minlog10padj <- -log10(res_df$padj)
+res_df$minlog10padj[is.na(res_df$minlog10padj)] <- NA
+
+# Add regulation direction
+res_df$Regulation <- ifelse(res_df$log2FoldChange >= opt$fc_threshold, "Up",
+                            ifelse(res_df$log2FoldChange <= -opt$fc_threshold,
+                                   "Down", "NS"))
+
+# Reorder columns
+res_df <- res_df[, c(ids_col, "Regulation",
+                     setdiff(colnames(res_df), c(ids_col, 
+                                                 "Regulation")))]
+
+# Save topTable as csv
+write.csv(res_df, opt$output, row.names = FALSE)
+cat("Full results saved to", opt$output, "\n")
+
+
+# Filter DEGs with adjusted p-value < p_threshold and absolute log2FoldChange > fc_threshold
+deg_df <- res_df[
+  res_df$padj <= opt$p_threshold & abs(res_df$log2FoldChange) >= opt$fc_threshold,
+  c(ids_col, "log2FoldChange", "Regulation")
+]
+# Filter out counts without ID
+deg_df <- deg_df[!is.na(deg_df[ids_col]),]
+
+# Save DEC as csv
+write.csv(deg_df, "DEG.csv", row.names = FALSE)
+cat("Filtered DEGs saved to", "DEG.csv", "\n")