@platforma-open/milaboratories.run-tcrdisco-enrichment.software 1.1.0

package/CHANGELOG.md

@@ -0,0 +1,7 @@
+# @platforma-open/milaboratories.run-tcrdisco-enrichment.software
+
+## 1.1.0
+
+### Minor Changes
+
+- ede2472: First block version

package/Dockerfile

@@ -0,0 +1,56 @@
+FROM r-base:4.4.2
+
+ENV R_VERSION=4.4.2
+ENV BIOCONDUCTOR_VERSION=3.20
+ENV RENV_VERSION=1.0.11
+ENV RENV_CONFIG_PPM_ENABLED=false
+ENV RENV_CONFIG_REPOS_OVERRIDE=https://cloud.r-project.org
+
+# Install system dependencies required for R packages
+RUN apt-get update && apt-get install -y \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libxml2-dev \
+    libcairo2-dev \
+    libgit2-dev \
+    default-libmysqlclient-dev \
+    libpq-dev \
+    libsasl2-dev \
+    libsqlite3-dev \
+    libssh2-1-dev \
+    unixodbc-dev \
+    libharfbuzz-dev \
+    libfribidi-dev \
+    libfreetype6-dev \
+    libpng-dev \
+    libtiff5-dev \
+    libjpeg-dev \
+    libgsl-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libpcre2-dev \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set working directory
+WORKDIR /app
+
+RUN R -e "install.packages('renv', repos = 'https://cloud.r-project.org')"
+
+# .Rprofile breaks renv restore
+# Copy only files that are needed
+COPY *.R .
+COPY ./renv.lock ./renv.lock
+
+# Have to use absolute paths because during execution the working directory will be changed
+# and realpath command does not work
+ENV RENV_PATHS_RENV=/app/renv
+ENV RENV_PATHS_LOCKFILE=/app/renv.lock
+
+RUN R --no-echo -e "renv::restore(clean = TRUE)"
+
+RUN echo "#!/bin/bash\nR --no-echo --no-restore -e \"renv::restore()\"\n\"\$@\"" > /app/run.sh
+RUN chmod +x /app/run.sh
+
+# Default command runs Rscript
+ENTRYPOINT ["/app/run.sh"]

package/dist/artifacts/get-enriched-frequencies/archive.json

@@ -0,0 +1 @@
+{"type":"R","platform":"linux-x64","registryURL":"https://bin.pl-open.science/","registryName":"platforma-open","remoteArtifactLocation":"software/platforma-open/milaboratories.run-tcrdisco-enrichment.software/get-enriched-frequencies/1.1.0.tgz","uploadPath":"software/platforma-open/milaboratories.run-tcrdisco-enrichment.software/get-enriched-frequencies/1.1.0.tgz"}

package/dist/artifacts/get-enriched-frequencies/docker_x64.json

@@ -0,0 +1 @@
+{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.run-tcrdisco-enrichment.software.get-enriched-frequencies.c8e04e155280"}

package/dist/artifacts/subset-assignment/archive.json

@@ -0,0 +1 @@
+{"type":"R","platform":"linux-x64","registryURL":"https://bin.pl-open.science/","registryName":"platforma-open","remoteArtifactLocation":"software/platforma-open/milaboratories.run-tcrdisco-enrichment.software/subset-assignment/1.1.0.tgz","uploadPath":"software/platforma-open/milaboratories.run-tcrdisco-enrichment.software/subset-assignment/1.1.0.tgz"}

package/dist/artifacts/subset-assignment/docker_x64.json

@@ -0,0 +1 @@
+{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.run-tcrdisco-enrichment.software.subset-assignment.eb67f96e9c9a"}

package/dist/artifacts/tcr-ab-pairs/archive.json

@@ -0,0 +1 @@
+{"type":"R","platform":"linux-x64","registryURL":"https://bin.pl-open.science/","registryName":"platforma-open","remoteArtifactLocation":"software/platforma-open/milaboratories.run-tcrdisco-enrichment.software/tcr-ab-pairs/1.1.0.tgz","uploadPath":"software/platforma-open/milaboratories.run-tcrdisco-enrichment.software/tcr-ab-pairs/1.1.0.tgz"}

package/dist/artifacts/tcr-ab-pairs/docker_x64.json

@@ -0,0 +1 @@
+{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.run-tcrdisco-enrichment.software.tcr-ab-pairs.2e1cbb240fae"}

package/dist/artifacts/tcr-disco/archive.json

@@ -0,0 +1 @@
+{"type":"R","platform":"linux-x64","registryURL":"https://bin.pl-open.science/","registryName":"platforma-open","remoteArtifactLocation":"software/platforma-open/milaboratories.run-tcrdisco-enrichment.software/tcr-disco/1.1.0.tgz","uploadPath":"software/platforma-open/milaboratories.run-tcrdisco-enrichment.software/tcr-disco/1.1.0.tgz"}

package/dist/artifacts/tcr-disco/docker_x64.json

@@ -0,0 +1 @@
+{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.run-tcrdisco-enrichment.software.tcr-disco.af738a23e37d"}

package/dist/tengo/software/get-enriched-frequencies.sw.json

@@ -0,0 +1 @@
+{"name":"@platforma-open/milaboratories.run-tcrdisco-enrichment.software:get-enriched-frequencies","docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.run-tcrdisco-enrichment.software.get-enriched-frequencies.c8e04e155280","entrypoint":[],"cmd":["/app/get-enriched-frequencies.R"],"pkg":"/app"},"binary":{"type":"R","registry":"platforma-open","package":"software/platforma-open/milaboratories.run-tcrdisco-enrichment.software/get-enriched-frequencies/1.1.0.tgz","cmd":["Rscript","{pkg}/get-enriched-frequencies.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","r-version":""},"toolset":"renv","dependencies":{}}}

package/dist/tengo/software/subset-assignment.sw.json

@@ -0,0 +1 @@
+{"name":"@platforma-open/milaboratories.run-tcrdisco-enrichment.software:subset-assignment","docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.run-tcrdisco-enrichment.software.subset-assignment.eb67f96e9c9a","entrypoint":[],"cmd":["/app/main.R"],"pkg":"/app"},"binary":{"type":"R","registry":"platforma-open","package":"software/platforma-open/milaboratories.run-tcrdisco-enrichment.software/subset-assignment/1.1.0.tgz","cmd":["Rscript","{pkg}/subset-assignment.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","r-version":""},"toolset":"renv","dependencies":{}}}

package/dist/tengo/software/tcr-ab-pairs.sw.json

@@ -0,0 +1 @@
+{"name":"@platforma-open/milaboratories.run-tcrdisco-enrichment.software:tcr-ab-pairs","docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.run-tcrdisco-enrichment.software.tcr-ab-pairs.2e1cbb240fae","entrypoint":[],"cmd":["/app/find-pairs.R"],"pkg":"/app"},"binary":{"type":"R","registry":"platforma-open","package":"software/platforma-open/milaboratories.run-tcrdisco-enrichment.software/tcr-ab-pairs/1.1.0.tgz","cmd":["Rscript","{pkg}/find-pairs.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","r-version":""},"toolset":"renv","dependencies":{}}}

package/dist/tengo/software/tcr-disco.sw.json

@@ -0,0 +1 @@
+{"name":"@platforma-open/milaboratories.run-tcrdisco-enrichment.software:tcr-disco","docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.run-tcrdisco-enrichment.software.tcr-disco.af738a23e37d","entrypoint":[],"cmd":["/app/main.R"],"pkg":"/app"},"binary":{"type":"R","registry":"platforma-open","package":"software/platforma-open/milaboratories.run-tcrdisco-enrichment.software/tcr-disco/1.1.0.tgz","cmd":["Rscript","{pkg}/main.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","r-version":""},"toolset":"renv","dependencies":{}}}

package/package.json

@@ -0,0 +1,116 @@
+{
+  "name": "@platforma-open/milaboratories.run-tcrdisco-enrichment.software",
+  "version": "1.1.0",
+  "type": "module",
+  "description": "Block Software: Run TCR Disco with R",
+  "block-software": {
+    "entrypoints": {
+      "subset-assignment": {
+        "binary": {
+          "artifact": {
+            "type": "R",
+            "registry": "platforma-open",
+            "environment": "@platforma-open/milaboratories.runenv-r-differential-expression:main",
+            "root": "./src/tcr-disco"
+          },
+          "cmd": [
+            "Rscript",
+            "{pkg}/subset-assignment.R"
+          ]
+        },
+        "docker": {
+          "artifact": {
+            "type": "docker",
+            "context": "./src/tcr-disco",
+            "dockerfile": "Dockerfile"
+          },
+          "cmd": [
+            "/app/main.R"
+          ]
+        }
+      },
+      "tcr-disco": {
+        "binary": {
+          "artifact": {
+            "type": "R",
+            "registry": "platforma-open",
+            "environment": "@platforma-open/milaboratories.runenv-r-differential-expression:main",
+            "root": "./src/tcr-disco"
+          },
+          "cmd": [
+            "Rscript",
+            "{pkg}/main.R"
+          ]
+        },
+        "docker": {
+          "artifact": {
+            "type": "docker",
+            "context": "./src/tcr-disco",
+            "dockerfile": "Dockerfile"
+          },
+          "cmd": [
+            "/app/main.R"
+          ]
+        }
+      },
+      "get-enriched-frequencies": {
+        "binary": {
+          "artifact": {
+            "type": "R",
+            "registry": "platforma-open",
+            "environment": "@platforma-open/milaboratories.runenv-r-differential-expression:main",
+            "root": "./src/tcr-disco"
+          },
+          "cmd": [
+            "Rscript",
+            "{pkg}/get-enriched-frequencies.R"
+          ]
+        },
+        "docker": {
+          "artifact": {
+            "type": "docker",
+            "context": "./src/tcr-disco",
+            "dockerfile": "Dockerfile"
+          },
+          "cmd": [
+            "/app/get-enriched-frequencies.R"
+          ]
+        }
+      },
+      "tcr-ab-pairs": {
+        "binary": {
+          "artifact": {
+            "type": "R",
+            "registry": "platforma-open",
+            "environment": "@platforma-open/milaboratories.runenv-r-differential-expression:main",
+            "root": "./src/tcr-disco"
+          },
+          "cmd": [
+            "Rscript",
+            "{pkg}/find-pairs.R"
+          ]
+        },
+        "docker": {
+          "artifact": {
+            "type": "docker",
+            "context": "./src/tcr-disco",
+            "dockerfile": "Dockerfile"
+          },
+          "cmd": [
+            "/app/find-pairs.R"
+          ]
+        }
+      }
+    }
+  },
+  "devDependencies": {
+    "@platforma-open/milaboratories.runenv-r-differential-expression": "^1.0.7",
+    "@platforma-sdk/package-builder": "^3.10.7"
+  },
+  "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/tcr-disco/find-pairs.R

@@ -0,0 +1,271 @@
+#!/usr/bin/env Rscript
+
+# Load required libraries
+suppressMessages(library("optparse"))
+#----------------------------------------
+
+# Required functions
+# 1.  generate fraction matrices
+get_fraction_matrix = function(main_table) {
+  # Generate frequency matrices for both alpha and beta
+  # Aggregate fractions by useSampleId and clonotypeKey
+  # Use clonotypeKey first to match group_by order
+  aggregated <- aggregate(fraction ~ clonotypeKey + useSampleId, 
+                          data = main_table, FUN = sum)
+
+  # Get unique values in the order they first appear in aggregated (matches group_by + summarise order)
+  unique_clonotypes <- unique(aggregated$clonotypeKey)
+  unique_samples <- unique(aggregated$useSampleId)
+
+  # Create matrix with proper dimensions and fill with 0
+  fraction_matrix <- matrix(0, 
+                        nrow = length(unique_clonotypes), 
+                        ncol = length(unique_samples),
+                        dimnames = list(unique_clonotypes, unique_samples))
+
+  # Fill matrix with aggregated values using match for efficiency
+  row_indices <- match(aggregated$clonotypeKey, unique_clonotypes)
+  col_indices <- match(aggregated$useSampleId, unique_samples)
+  fraction_matrix[cbind(row_indices, col_indices)] <- aggregated$fraction
+
+  # Ensure it's a numeric matrix
+  fraction_matrix <- as.matrix(fraction_matrix)
+  fraction_matrix[is.na(fraction_matrix)] <- 0
+
+  return (fraction_matrix)
+}
+
+# 2.  find pairs
+find_pairs = function(deg_alpha_table, deg_beta_table, metadata_table, 
+      contrast_col, alpha_matrix, beta_matrix, num) {
+  # samples related to the selected numerator
+  alpha_clonotypes <- unique(deg_alpha_table[deg_alpha_table$Numerator == num, "clonotypeKey"])
+  beta_clonotypes <- unique(deg_beta_table[deg_beta_table$Numerator == num, "clonotypeKey"])
+  numerator_samples <- metadata_table[metadata_table[,contrast_col] == num, "useSampleId"]
+  alpha_matrix <- alpha_matrix[alpha_clonotypes, 
+      colnames(alpha_matrix)[colnames(alpha_matrix) %in% numerator_samples], drop = FALSE]
+  beta_matrix <- beta_matrix[beta_clonotypes, 
+      colnames(beta_matrix)[colnames(beta_matrix) %in% numerator_samples], drop = FALSE]
+
+  # merge TRA and TRB clonotypes into one dataframe
+  fraction_table_ab <- t(rbind(alpha_matrix, beta_matrix))
+
+  # Generate all possible alpha-beta pairs using base R
+  pairs_grid <- expand.grid(
+    tra = rownames(alpha_matrix),
+    trb = rownames(beta_matrix),
+    stringsAsFactors = FALSE
+  )
+
+  # Run correlation tests for each pair
+  test_results <- mapply(function(tra, trb) {
+    df_small <- fraction_table_ab[, c(tra, trb), drop = FALSE]
+    # Check whether both chains are present or absent within replicates
+    if (all(rowSums(df_small == 0) != 1)) {
+      cor.test(df_small[, 1], df_small[, 2])
+    } else {
+      NULL
+    }
+  }, pairs_grid$tra, pairs_grid$trb, SIMPLIFY = FALSE)
+
+  # Filter out NULL results and extract estimates and p-values
+  valid_indices <- !sapply(test_results, is.null)
+  predicted_pairs <- pairs_grid[valid_indices, , drop = FALSE]
+  predicted_pairs$estimate <- sapply(test_results[valid_indices], function(x) x$estimate)
+  predicted_pairs$p.value <- sapply(test_results[valid_indices], function(x) x$p.value)
+
+  # Perform FDR adjustment and filter by R & FDR threshold
+  predicted_pairs$p.adj <- p.adjust(predicted_pairs$p.value, method = "fdr")
+  # predicted_pairs <- predicted_pairs[
+  #   predicted_pairs$p.adj <= fdr_cut & predicted_pairs$estimate >= estimate_cut,
+  #   , drop = FALSE
+  # ]
+
+  # Add contrast column
+  predicted_pairs["Numerator"] = num
+
+  return (predicted_pairs)
+}
+
+#----------------------------------------
+
+# Main code
+
+# Parse command line arguments
+option_list <- list(
+  make_option(c("--main_alpha"),
+    type = "character", default = "mainAlpha.tsv",
+    help = "Path to main TCR alpha clonotypes TSV file", metavar = "character"
+  ),
+  make_option(c("--main_beta"),
+    type = "character", default = "mainBeta.tsv",
+    help = "Path to main TCR beta clonotypes TSV file", metavar = "character"
+  ),
+  make_option(c("--da_alpha"),
+    type = "character", default = "daAlpha.csv",
+    help = "Path to DA alpha CSV file", metavar = "character"
+  ),
+  make_option(c("--da_beta"),
+    type = "character", default = "daBeta.csv",
+    help = "Path to DA beta CSV file", metavar = "character"
+  ),
+  make_option(c("--metadata"),
+    type = "character", default = "metadata.tsv",
+    help = "Path to metadata TSV file", metavar = "character"
+  ),
+  make_option(c("-t", "--contrast_col"),
+    type = "character", default = NULL,
+    help = "Column name in metadata for the contrast",
+    metavar = "character"
+  ),
+  make_option(c("--sample_id_col"),
+    type = "character", default = NULL,
+    help = "Column name in metadata for the sample ID",
+    metavar = "character"
+  ),
+  make_option(c("-f", "--fc_threshold"),
+    type = "double", default = 0.5,
+    help = "Log2(FC) threshold for significance"
+  ),
+  make_option(c("-p", "--p_threshold"),
+    type = "double", default = 0.05,
+    help = "Adjusted p-value threshold for significance"
+  ),
+  make_option(c("-o", "--output"),
+    type = "character",
+    default = ".",
+    help = "Output folder for TSV results", metavar = "character"
+  )
+)
+
+opt_parser <- OptionParser(option_list = option_list)
+opt <- parse_args(opt_parser)
+
+# Get input data
+main_alpha <- opt$main_alpha
+main_beta <- opt$main_beta
+da_alpha <- opt$da_alpha
+da_beta <- opt$da_beta
+metadata <- opt$metadata
+contrast_col <- opt$contrast_col
+sample_id_col <- opt$sample_id_col
+fc_cut <- opt$fc_threshold
+fdr_cut <- opt$p_threshold
+output_folder <- opt$output
+
+# test
+# metadata <- "./metadata.tsv"
+# main_alpha <- "./mainAlpha.tsv"
+# main_beta <- "./mainBeta.tsv"
+# da_alpha <- "./daAlpha.csv"
+# da_beta <- "./daBeta.csv"
+# contrast_col <- "ag"
+# output_folder <- "./resultsPairing"
+# sample_id_col <- "Barcode ID"
+
+# Get from platforma
+# @TODO: Filters are not yet script-specific, implement them separately for DA and pairing
+# fdr_cut <- 0.05
+# estimate_cut <- 0.95
+
+## Control prints
+print(paste("metadata file: ", metadata))
+print(paste("main alpha file: ", main_alpha))
+print(paste("main beta file: ", main_beta))
+print(paste("da alpha file: ", da_alpha))
+print(paste("da beta file: ", da_beta))
+print(paste("contrast column: ", contrast_col))
+print(paste("sample id column: ", sample_id_col))
+print(paste("fc threshold: ", fc_cut))
+print(paste("fdr threshold: ", fdr_cut))
+print(paste("output folder: ", output_folder))
+
+## 1.1. TCR Discovery
+# Get alpha/beta DEG tables
+deg_alpha_table <- read.csv(da_alpha, header = TRUE, sep = ",", stringsAsFactors = FALSE)
+deg_beta_table <- read.csv(da_beta, header = TRUE, sep = ",", stringsAsFactors = FALSE)
+
+if (nrow(deg_alpha_table) == 0 || nrow(deg_beta_table) == 0) {
+  print("Warning: The DA alpha or beta tables are empty. No pairs will be found.")
+
+  # Create an emtpy output table with sall the required columns
+  required_cols <- c("Numerator", "tra", "trb", "estimate", "p.value", "p.adj", "tra_CDR3aa", "tra_VGene", "trb_CDR3aa", "trb_VGene", "is_max_correlation")
+  empty_table <- data.frame(matrix(ncol = length(required_cols), nrow = 0))
+  colnames(empty_table) <- required_cols
+  predicted_pairs_all <- empty_table
+
+} else {
+  # Load metadata and main alpha/beta tables
+  metadata_table <- read.table(metadata, header = TRUE, sep = "\t", stringsAsFactors = FALSE, check.names = FALSE)
+  main_alpha_table <- read.table(main_alpha, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
+  main_beta_table <- read.table(main_beta, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
+
+  # check if sample_id_col is in metadata_table and if it has less values than internalSampleId
+  main_alpha_table$useSampleId <- main_alpha_table$internalSampleId
+  main_beta_table$useSampleId <- main_beta_table$internalSampleId
+  if (sample_id_col %in% colnames(metadata_table)) {
+    if (length(unique(metadata_table[, sample_id_col])) < length(unique(metadata_table$internalSampleId))) {
+      # Add original sample ID to the alpha and beta tables
+      main_alpha_table$useSampleId <- metadata_table[match(main_alpha_table$internalSampleId, metadata_table$internalSampleId), sample_id_col]
+      main_beta_table$useSampleId <- metadata_table[match(main_beta_table$internalSampleId, metadata_table$internalSampleId), sample_id_col]
+
+      metadata_table$useSampleId <- metadata_table[, sample_id_col]
+    } 
+  }
+
+  # Make sure we have the same set of samples to compare
+  if (!identical(sort(unique(main_alpha_table$useSampleId)), sort(unique(main_beta_table$useSampleId)))) {
+    stop("Error: The sets of samples in the alpha and beta tables are not the same")
+  }
+
+  # Filter main tables to only include DEG clonotypes to reduce memory and processing time
+  # We will loose samples, so it's important to have it after the check above
+  deg_alpha_clonotypes <- unique(deg_alpha_table$clonotypeKey)
+  deg_beta_clonotypes <- unique(deg_beta_table$clonotypeKey)
+  main_alpha_table <- main_alpha_table[main_alpha_table$clonotypeKey %in% deg_alpha_clonotypes, ]
+  main_beta_table <- main_beta_table[main_beta_table$clonotypeKey %in% deg_beta_clonotypes, ]
+
+  # Get alpha/beta fraction matrices
+  alpha_matrix <- get_fraction_matrix(main_alpha_table)
+  beta_matrix <- get_fraction_matrix(main_beta_table)
+
+  # Get all possible values from Numerator column in both tables
+  numerators <- unique(c(deg_alpha_table$Numerator, deg_beta_table$Numerator))
+
+  # Find pairs per numerator and comine results into one table
+  predicted_pairs_all <- data.frame()
+  for (num in numerators) {
+    predicted_pairs <- find_pairs(deg_alpha_table, deg_beta_table, metadata_table, 
+        contrast_col, alpha_matrix, beta_matrix, num)
+    predicted_pairs_all <- rbind(predicted_pairs_all, predicted_pairs)
+  }
+
+  # Filter out negative correlations
+  predicted_pairs_all <- predicted_pairs_all[predicted_pairs_all$estimate >= 0, ]
+
+  
+  # Add TRA and TRB CDR3 aa and VGene data
+  ## Match tra column with alpha table 
+  alpha_match_idx <- match(predicted_pairs_all$tra, main_alpha_table$clonotypeKey)
+  predicted_pairs_all$tra_CDR3aa <- main_alpha_table$CDR3aa[alpha_match_idx]
+  predicted_pairs_all$tra_VGene <- main_alpha_table$VGene[alpha_match_idx]
+  ## Match trb column with beta table
+  beta_match_idx <- match(predicted_pairs_all$trb, main_beta_table$clonotypeKey)
+  predicted_pairs_all$trb_CDR3aa <- main_beta_table$CDR3aa[beta_match_idx]
+  predicted_pairs_all$trb_VGene <- main_beta_table$VGene[beta_match_idx]
+
+  # Add column indicating if this pair's correlation is the maximum for either tra or trb
+  predicted_pairs_all$is_max_correlation <- 
+    (predicted_pairs_all$estimate == ave(predicted_pairs_all$estimate, predicted_pairs_all$tra, FUN = max)) |
+    (predicted_pairs_all$estimate == ave(predicted_pairs_all$estimate, predicted_pairs_all$trb, FUN = max))
+  predicted_pairs_all$is_max_correlation[predicted_pairs_all$is_max_correlation == TRUE] <- "max"
+  predicted_pairs_all$is_max_correlation[predicted_pairs_all$is_max_correlation == FALSE] <- "not_max"
+  
+  # Order by tra
+  predicted_pairs_all <- predicted_pairs_all[order(predicted_pairs_all$tra), ]
+}
+
+#save ft_ and ct_filtered in the output_folder
+write.table(predicted_pairs_all, paste0(output_folder, "/ab_pairs.tsv"), 
+                sep = "\t", quote = F, row.names = F)
+

package/src/tcr-disco/get-enriched-frequencies.R

@@ -0,0 +1,102 @@
+#!/usr/bin/env Rscript
+
+# Load required libraries
+suppressMessages(library("optparse"))
+#----------------------------------------
+
+# Main code
+
+# Parse command line arguments
+option_list <- list(
+  make_option(c("--main_alpha"),
+    type = "character", default = "mainAlpha.tsv",
+    help = "Path to main TCR alpha clonotypes TSV file", metavar = "character"
+  ),
+  make_option(c("--main_beta"),
+    type = "character", default = "mainBeta.tsv",
+    help = "Path to main TCR beta clonotypes TSV file", metavar = "character"
+  ),
+  make_option(c("--da_alpha"),
+    type = "character", default = "daAlpha.csv",
+    help = "Path to DA alpha CSV file", metavar = "character"
+  ),
+  make_option(c("--da_beta"),
+    type = "character", default = "daBeta.csv",
+    help = "Path to DA beta CSV file", metavar = "character"
+  ),
+  make_option(c("-o", "--output"),
+    type = "character",
+    default = ".",
+    help = "Output folder for TSV results", metavar = "character"
+  )
+)
+
+opt_parser <- OptionParser(option_list = option_list)
+opt <- parse_args(opt_parser)
+
+# Get input data
+main_alpha <- opt$main_alpha
+main_beta <- opt$main_beta
+da_alpha <- opt$da_alpha
+da_beta <- opt$da_beta
+output_folder <- opt$output
+
+# test
+# main_alpha <- "./mainAlpha.tsv"
+# main_beta <- "./mainBeta.tsv"
+# da_alpha <- "./DA_alpha.csv"
+# da_beta <- "./DA_beta.csv"
+# output_folder <- "./resultsPairing"
+
+
+## 1.1. TCR Discovery
+# Load metadata
+main_alpha_table <- read.table(main_alpha, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
+main_beta_table <- read.table(main_beta, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
+
+# Get alpha/beta DEG tables
+deg_alpha_table <- read.csv(da_alpha, header = TRUE, sep = ",", stringsAsFactors = FALSE)
+deg_beta_table <- read.csv(da_beta, header = TRUE, sep = ",", stringsAsFactors = FALSE)
+
+# Keep only DA clonotypes from main tables
+main_alpha_table <- main_alpha_table[main_alpha_table$clonotypeKey %in% unique(deg_alpha_table$clonotypeKey), ]
+main_beta_table <- main_beta_table[main_beta_table$clonotypeKey %in% unique(deg_beta_table$clonotypeKey), ]
+
+# Store the tables
+if (!dir.exists(output_folder)) {
+  dir.create(output_folder, recursive = TRUE)
+}
+
+if ("subset" %in% colnames(main_alpha_table)) {
+  keep_cols1 <- c("internalSampleId", "clonotypeKey", "fraction", "subset")
+  keep_cols2 <- c("clonotypeKey", "subset")
+} else {
+  keep_cols1 <- c("internalSampleId", "clonotypeKey", "fraction")
+  keep_cols2 <- c("clonotypeKey")
+}
+write.table(main_alpha_table[, keep_cols1], 
+                paste0(output_folder, "/main_alpha_frequencies.tsv"), 
+                sep = "\t", quote = F, row.names = F)
+write.table(main_beta_table[, keep_cols1], 
+                paste0(output_folder, "/main_beta_frequencies.tsv"), 
+                sep = "\t", quote = F, row.names = F)
+
+if ("subset" %in% colnames(main_alpha_table)) {
+  # store clonotype to subset mapping removing repeated lines
+  clonotype_to_subset_alpha <- unique(main_alpha_table[, c("clonotypeKey", "subset")])
+  clonotype_to_subset_beta <- unique(main_beta_table[, c("clonotypeKey", "subset")])
+
+  write.table(clonotype_to_subset_alpha, paste0(output_folder, "/clonotype_to_subset_alpha.tsv"), 
+    sep = "\t", quote = F, row.names = F)
+  write.table(clonotype_to_subset_beta, paste0(output_folder, "/clonotype_to_subset_beta.tsv"), 
+    sep = "\t", quote = F, row.names = F)
+} else {
+  # Create empty tables
+  clonotype_to_subset_alpha <- data.frame(clonotypeKey = character(), subset = character())
+  clonotype_to_subset_beta <- data.frame(clonotypeKey = character(), subset = character())
+
+  write.table(clonotype_to_subset_alpha, paste0(output_folder, "/clonotype_to_subset_alpha.tsv"), 
+    sep = "\t", quote = F, row.names = F)
+  write.table(clonotype_to_subset_beta, paste0(output_folder, "/clonotype_to_subset_beta.tsv"), 
+    sep = "\t", quote = F, row.names = F)
+}