--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.R	Fri Jun 10 10:18:24 2022 +0000
@@ -0,0 +1,149 @@
+library(recetox.aplcms)
+
+align_features <- function(sample_names, ...) {
+    aligned <- feature.align(...)
+    feature_names <- seq_len(nrow(aligned$pk.times))
+
+  list(
+    mz_tolerance = as.numeric(aligned$mz.tol),
+    rt_tolerance = as.numeric(aligned$chr.tol),
+    rt_crosstab = as_feature_crosstab(feature_names, sample_names, aligned$pk.times),
+    int_crosstab = as_feature_crosstab(feature_names, sample_names, aligned$aligned.ftrs)
+    )
+}
+
+get_sample_name <- function(filename) {
+    tools::file_path_sans_ext(basename(filename))
+}
+
+as_feature_crosstab <- function(feature_names, sample_names, data) {
+  colnames(data) <- c("mz", "rt", "mz_min", "mz_max", sample_names)
+  rownames(data) <- feature_names
+  as.data.frame(data)
+}
+
+as_feature_sample_table <- function(rt_crosstab, int_crosstab) {
+  feature_names <- rownames(rt_crosstab)
+  sample_names <- colnames(rt_crosstab)[- (1:4)]
+
+  feature_table <- data.frame(
+    feature = feature_names,
+    mz = rt_crosstab[, 1],
+    rt = rt_crosstab[, 2]
+  )
+
+  # series of conversions to produce a table type from data.frame
+  rt_crosstab <- as.table(as.matrix(rt_crosstab[, - (1:4)]))
+  int_crosstab <- as.table(as.matrix(int_crosstab[, - (1:4)]))
+
+  crosstab_axes <- list(feature = feature_names, sample = sample_names)
+  dimnames(rt_crosstab) <- dimnames(int_crosstab) <- crosstab_axes
+
+  x <- as.data.frame(rt_crosstab, responseName = "sample_rt")
+  y <- as.data.frame(int_crosstab, responseName = "sample_intensity")
+
+  data <- merge(x, y, by = c("feature", "sample"))
+  data <- merge(feature_table, data, by = "feature")
+  data
+}
+
+load_features <- function(files) {
+    files_list <- sort_samples_by_acquisition_number(files)
+    features <- lapply(files_list, arrow::read_parquet)
+    features <- lapply(features, as.matrix)
+    return(features)
+}
+
+save_data_as_parquet_files <- function(data, subdir) {
+  dir.create(subdir)
+  for (i in 0:(length(data) - 1)) {
+    filename <- file.path(subdir, paste0(subdir, "_features_", i, ".parquet"))
+    arrow::write_parquet(as.data.frame(data[i + 1]), filename)
+  }
+}
+
+save_aligned_features <- function(aligned, rt_file, int_file, tol_file) {
+  arrow::write_parquet(as.data.frame(aligned$rt_crosstab), rt_file)
+  arrow::write_parquet(as.data.frame(aligned$int_crosstab), int_file)
+
+  mz_tolerance <- c(aligned$mz_tolerance)
+  rt_tolerance <- c(aligned$rt_tolerance)
+  arrow::write_parquet(data.frame(mz_tolerance, rt_tolerance), tol_file)
+}
+
+load_aligned_features <- function(rt_file, int_file, tol_file) {
+  rt_cross_table <- arrow::read_parquet(rt_file)
+  int_cross_table <- arrow::read_parquet(int_file)
+  tolerances_table <- arrow::read_parquet(tol_file)
+
+  result <- list()
+  result$mz_tolerance <- tolerances_table$mz_tolerance
+  result$rt_tolerance <- tolerances_table$rt_tolerance
+  result$rt_crosstab <- rt_cross_table
+  result$int_crosstab <- int_cross_table
+  return(result)
+}
+
+recover_signals <- function(cluster,
+                            filenames,
+                            extracted,
+                            corrected,
+                            aligned,
+                            mz_tol = 1e-05,
+                            mz_range = NA,
+                            rt_range = NA,
+                            use_observed_range = TRUE,
+                            min_bandwidth = NA,
+                            max_bandwidth = NA,
+                            recover_min_count = 3) {
+  if (!is(cluster, "cluster")) {
+    cluster <- parallel::makeCluster(cluster)
+    on.exit(parallel::stopCluster(cluster))
+  }
+
+  clusterExport(cluster, c("extracted", "corrected", "aligned", "recover.weaker"))
+  clusterEvalQ(cluster, library("splines"))
+
+  recovered <- parLapply(cluster, seq_along(filenames), function(i) {
+    recover.weaker(
+      loc = i,
+      filename = filenames[[i]],
+      this.f1 = extracted[[i]],
+      this.f2 = corrected[[i]],
+      pk.times = aligned$rt_crosstab,
+      aligned.ftrs = aligned$int_crosstab,
+      orig.tol = mz_tol,
+      align.mz.tol = aligned$mz_tolerance,
+      align.chr.tol = aligned$rt_tolerance,
+      mz.range = mz_range,
+      chr.range = rt_range,
+      use.observed.range = use_observed_range,
+      bandwidth = 0.5,
+      min.bw = min_bandwidth,
+      max.bw = max_bandwidth,
+      recover.min.count = recover_min_count
+    )
+  })
+
+  feature_table <- aligned$rt_crosstab[, 1:4]
+  rt_crosstab <- cbind(feature_table, sapply(recovered, function(x) x$this.times))
+  int_crosstab <- cbind(feature_table, sapply(recovered, function(x) x$this.ftrs))
+
+  feature_names <- rownames(feature_table)
+  sample_names <- colnames(aligned$rt_crosstab[, - (1:4)])
+
+  list(
+    extracted_features = lapply(recovered, function(x) x$this.f1),
+    corrected_features = lapply(recovered, function(x) x$this.f2),
+    rt_crosstab = as_feature_crosstab(feature_names, sample_names, rt_crosstab),
+    int_crosstab = as_feature_crosstab(feature_names, sample_names, int_crosstab)
+  )
+}
+
+create_feature_sample_table <- function(features) {
+  table <- as_feature_sample_table(
+      rt_crosstab = features$rt_crosstab,
+      int_crosstab = features$int_crosstab
+  )
+  return(table)
+}