--- a/diffbind.R	Wed Nov 18 12:54:07 2020 +0000
+++ b/diffbind.R	Fri Dec 15 19:39:14 2023 +0000
@@ -1,14 +1,15 @@
 ## Setup R error handling to go to stderr
-options(show.error.messages = F, error = function() {
-    cat(geterrmessage(), file = stderr()); q("no", 1, F)
+options(show.error.messages = FALSE, error = function() {
+  cat(geterrmessage(), file = stderr())
+  q("no", 1, FALSE)
 })
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 
 suppressPackageStartupMessages({
-    library("getopt")
-    library("DiffBind")
-    library("rjson")
+  library("getopt")
+  library("DiffBind")
+  library("rjson")
 })
 
 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
@@ -17,28 +18,28 @@
 #get options, using the spec as defined by the enclosed list.
 #we read the options from the default: commandArgs(TRUE).
 spec <- matrix(c(
-    "infile", "i", 1, "character",
-    "outfile", "o", 1, "character",
-    "scorecol", "n", 1, "integer",
-    "lowerbetter", "l", 1, "logical",
-    "summits", "s", 1, "integer",
-    "th", "t", 1, "double",
-    "format", "f", 1, "character",
-    "plots", "p", 2, "character",
-    "bmatrix", "b", 0, "logical",
-    "rdaOpt", "r", 0, "logical",
-    "infoOpt", "a", 0, "logical",
-    "verbose", "v", 2, "integer",
-    "help", "h", 0, "logical"
-), byrow = TRUE, ncol = 4);
+  "infile", "i", 1, "character",
+  "outfile", "o", 1, "character",
+  "scorecol", "n", 1, "integer",
+  "lowerbetter", "l", 1, "logical",
+  "summits", "s", 1, "integer",
+  "th", "t", 1, "double",
+  "format", "f", 1, "character",
+  "plots", "p", 2, "character",
+  "bmatrix", "b", 0, "logical",
+  "rdaOpt", "r", 0, "logical",
+  "infoOpt", "a", 0, "logical",
+  "verbose", "v", 2, "integer",
+  "help", "h", 0, "logical"
+), byrow = TRUE, ncol = 4)
 
-opt <- getopt(spec);
+opt <- getopt(spec)
 
 # if help was asked for print a friendly message
 # and exit with a non-zero error code
 if (!is.null(opt$help)) {
-    cat(getopt(spec, usage = TRUE));
-    q(status = 1);
+  cat(getopt(spec, usage = TRUE))
+  q(status = 1)
 }
 
 parser <- newJSONParser()
@@ -54,28 +55,31 @@
 samples <- sapply(strsplit(peaks, "-"), `[`, 2)
 
 if (length(ctrls) != 0) {
-    sample_table <- data.frame(SampleID = samples,
-                        Condition = groups,
-                        bamReads = bams,
-                        bamControl = ctrls,
-                        Peaks = peaks,
-                        Tissue = samples) # using "Tissue" column to display ids as labels in PCA plot
+  sample_table <- data.frame(
+    SampleID = samples,
+    Condition = groups,
+    bamReads = bams,
+    bamControl = ctrls,
+    Peaks = peaks,
+    Tissue = samples
+  ) # using "Tissue" column to display ids as labels in PCA plot
 } else {
-
-    sample_table <- data.frame(SampleID = samples,
-                        Replicate = samples,
-                        Condition = groups,
-                        bamReads = bams,
-                        Peaks = peaks,
-                        Tissue = samples)
+  sample_table <- data.frame(
+    SampleID = samples,
+    Replicate = samples,
+    Condition = groups,
+    bamReads = bams,
+    Peaks = peaks,
+    Tissue = samples
+  )
 }
 
 sample <- dba(sampleSheet = sample_table, peakFormat = "bed", scoreCol = opt$scorecol, bLowerScoreBetter = opt$lowerbetter)
 
 if (!is.null(opt$summits)) {
-    sample_count <- dba.count(sample, summits = opt$summits)
+  sample_count <- dba.count(sample, summits = opt$summits)
 } else {
-    sample_count <- dba.count(sample)
+  sample_count <- dba.count(sample)
 }
 
 sample_contrast <- dba.contrast(sample_count, categories = DBA_CONDITION, minMembers = 2)
@@ -84,74 +88,82 @@
 
 # Generate plots
 if (!is.null(opt$plots)) {
-    pdf(opt$plots)
-    orvals <- dba.plotHeatmap(sample_analyze, contrast = 1, correlations = FALSE, cexCol = 0.8, th = opt$th)
-    dba.plotPCA(sample_analyze, contrast = 1, th = opt$th, label = DBA_TISSUE, labelSize = 0.3)
-    dba.plotMA(sample_analyze, th = opt$th)
-    dba.plotVolcano(sample_analyze, th = opt$th)
-    dba.plotBox(sample_analyze, th = opt$th)
-    dev.off()
+  pdf(opt$plots)
+  orvals <- dba.plotHeatmap(sample_analyze, contrast = 1, correlations = FALSE, cexCol = 0.8, th = opt$th)
+  dba.plotPCA(sample_analyze, contrast = 1, th = opt$th, label = DBA_TISSUE, labelSize = 0.3)
+  dba.plotMA(sample_analyze, th = opt$th)
+  dba.plotVolcano(sample_analyze, th = opt$th)
+  dba.plotBox(sample_analyze, th = opt$th)
+  dev.off()
 }
 
 # Output differential binding sites
 res_sorted <- diff_bind[order(diff_bind$FDR), ]
 # Convert from GRanges (1-based) to 0-based format (adapted from https://www.biostars.org/p/89341/)
 if (opt$format == "bed") {
-    res_sorted  <- data.frame(Chrom = seqnames(res_sorted),
-        Start = start(res_sorted) - 1,
-        End = end(res_sorted),
-        Name = rep("DiffBind", length(res_sorted)),
-        Score = rep("0", length(res_sorted)),
-        Strand = gsub("\\*", ".", strand(res_sorted)))
+  res_sorted  <- data.frame(
+    Chrom = seqnames(res_sorted),
+    Start = start(res_sorted) - 1,
+    End = end(res_sorted),
+    Name = rep("DiffBind", length(res_sorted)),
+    Score = rep("0", length(res_sorted)),
+    Strand = gsub("\\*", ".", strand(res_sorted))
+  )
 } else if (opt$format == "interval") {
-     # Output as interval
-    df <- as.data.frame(res_sorted)
-    extrainfo <- NULL
-    for (i in seq_len(nrow(df))) {
-        extrainfo[i] <- paste0(c(df$width[i], df[i, 6:ncol(df)]), collapse = "|")
-    }
-    res_sorted  <- data.frame(Chrom = seqnames(res_sorted),
-        Start = start(res_sorted) - 1,
-        End = end(res_sorted),
-        Name = rep("DiffBind", length(res_sorted)),
-        Score = rep("0", length(res_sorted)),
-        Strand = gsub("\\*", ".", strand(res_sorted)),
-        Comment = extrainfo)
+  # Output as interval
+  df <- as.data.frame(res_sorted)
+  extrainfo <- NULL
+  for (i in seq_len(nrow(df))) {
+    extrainfo[i] <- paste0(c(df$width[i], df[i, 6:ncol(df)]), collapse = "|")
+  }
+  res_sorted  <- data.frame(
+    Chrom = seqnames(res_sorted),
+    Start = start(res_sorted) - 1,
+    End = end(res_sorted),
+    Name = rep("DiffBind", length(res_sorted)),
+    Score = rep("0", length(res_sorted)),
+    Strand = gsub("\\*", ".", strand(res_sorted)),
+    Comment = extrainfo
+  )
 } else {
-    # Output as 0-based tabular
-    res_sorted <- data.frame(Chrom = seqnames(res_sorted),
-        Start = start(res_sorted) - 1,
-        End = end(res_sorted),
-        Name = rep("DiffBind", length(res_sorted)),
-        Score = rep("0", length(res_sorted)),
-        Strand = gsub("\\*", ".", strand(res_sorted)),
-        mcols(res_sorted))
+  # Output as 0-based tabular
+  res_sorted <- data.frame(
+    Chrom = seqnames(res_sorted),
+    Start = start(res_sorted) - 1,
+    End = end(res_sorted),
+    Name = rep("DiffBind", length(res_sorted)),
+    Score = rep("0", length(res_sorted)),
+    Strand = gsub("\\*", ".", strand(res_sorted)),
+    mcols(res_sorted)
+  )
 }
 write.table(res_sorted, file = opt$outfile, sep = "\t", quote = FALSE, row.names = FALSE)
 
 # Output binding affinity scores
 if (!is.null(opt$bmatrix)) {
-    bmat <- dba.peakset(sample_count, bRetrieve = TRUE, DataType = DBA_DATA_FRAME)
-    # Output as 0-based tabular
-    bmat <- data.frame(Chrom = bmat[, 1],
-        Start = bmat[, 2] - 1,
-        End = bmat[, 3],
-        bmat[, 4:ncol(bmat)])
-    write.table(bmat, file = "bmatrix.tab", sep = "\t", quote = FALSE, row.names = FALSE)
+  bmat <- dba.peakset(sample_count, bRetrieve = TRUE, DataType = DBA_DATA_FRAME)
+  # Output as 0-based tabular
+  bmat <- data.frame(
+    Chrom = bmat[, 1],
+    Start = bmat[, 2] - 1,
+    End = bmat[, 3],
+    bmat[, 4:ncol(bmat)]
+  )
+  write.table(bmat, file = "bmatrix.tab", sep = "\t", quote = FALSE, row.names = FALSE)
 }
 
 # Output RData file
 if (!is.null(opt$rdaOpt)) {
-    save.image(file = "DiffBind_analysis.RData")
+  save.image(file = "DiffBind_analysis.RData")
 }
 
 # Output analysis info
 if (!is.null(opt$infoOpt)) {
-    info <- "DiffBind_analysis_info.txt"
-    cat("dba.count Info\n\n", file = info, append = TRUE)
-    capture.output(sample, file = info, append = TRUE)
-    cat("\ndba.analyze Info\n\n", file = info, append = TRUE)
-    capture.output(sample_analyze, file = info, append = TRUE)
-    cat("\nSessionInfo\n\n", file = info, append = TRUE)
-    capture.output(sessionInfo(), file = info, append = TRUE)
+  info <- "DiffBind_analysis_info.txt"
+  cat("dba.count Info\n\n", file = info, append = TRUE)
+  capture.output(sample, file = info, append = TRUE)
+  cat("\ndba.analyze Info\n\n", file = info, append = TRUE)
+  capture.output(sample_analyze, file = info, append = TRUE)
+  cat("\nSessionInfo\n\n", file = info, append = TRUE)
+  capture.output(sessionInfo(), file = info, append = TRUE)
 }