--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/waveica_wrapper.R	Wed Mar 23 11:35:30 2022 +0000
@@ -0,0 +1,155 @@
+waveica <- function(data,
+                    wavelet_filter,
+                    wavelet_length,
+                    k,
+                    t,
+                    t2,
+                    alpha,
+                    exclude_blanks) {
+
+  # get input from the Galaxy, preprocess data
+  data <- read.csv(data, header = TRUE)
+
+  required_columns <- c("sampleName", "class", "sampleType", "injectionOrder", "batch")
+  verify_input_dataframe(data, required_columns)
+
+  data <- sort_by_injection_order(data)
+
+  # separate data into features, batch and group
+  feature_columns <- colnames(data)[!colnames(data) %in% required_columns]
+  features <- data[, feature_columns]
+  group <- enumerate_groups(as.character(data$sampleType))
+  batch <- data$batch
+
+  # run WaveICA
+  features <- recetox.waveica::waveica(
+    data = features,
+    wf = get_wf(wavelet_filter, wavelet_length),
+    batch = batch,
+    group = group,
+    K = k,
+    t = t,
+    t2 = t2,
+    alpha = alpha
+  )
+
+  data[, feature_columns] <- features
+
+  # remove blanks from dataset
+  if (exclude_blanks) {
+    data <- exclude_group(data, group)
+  }
+
+  return(data)
+}
+
+
+waveica_singlebatch <- function(data,
+                                wavelet_filter,
+                                wavelet_length,
+                                k,
+                                alpha,
+                                cutoff,
+                                exclude_blanks) {
+
+  # get input from the Galaxy, preprocess data
+  data <- read.csv(data, header = TRUE)
+
+  required_columns <- c("sampleName", "class", "sampleType", "injectionOrder")
+  optional_columns <- c("batch")
+  verify_input_dataframe(data, required_columns)
+
+  data <- sort_by_injection_order(data)
+
+  feature_columns <- colnames(data)[!colnames(data) %in% c(required_columns, optional_columns)]
+  features <- data[, feature_columns]
+  injection_order <- data$injectionOrder
+
+  # run WaveICA
+  features <- recetox.waveica::waveica_nonbatchwise(
+    data = features,
+    wf = get_wf(wavelet_filter, wavelet_length),
+    injection_order = injection_order,
+    K = k,
+    alpha = alpha,
+    cutoff = cutoff
+  )
+
+  data[, feature_columns] <- features
+
+  # remove blanks from dataset
+  if (exclude_blanks) {
+    data <- exclude_group(data, group)
+  }
+
+  return(data)
+}
+
+
+sort_by_injection_order <- function(data) {
+  if ("batch" %in% colnames(data)) {
+    data <- data[order(data[, "batch"],
+      data[, "injectionOrder"],
+      decreasing = FALSE
+    ), ]
+  } else {
+    data <- data[order(data[, "injectionOrder"],
+      decreasing = FALSE
+    ), ]
+  }
+  return(data)
+}
+
+
+verify_input_dataframe <- function(data, required_columns) {
+  if (anyNA(data)) {
+    stop("Error: dataframe cannot contain NULL values!
+Make sure that your dataframe does not contain empty cells")
+  } else if (!all(required_columns %in% colnames(data))) {
+    stop("Error: missing metadata!
+Make sure that the following columns are present in your dataframe: ", paste(required_columns, collapse = ", "))
+  }
+}
+
+
+# Match group labels with [blank/sample/qc] and enumerate them
+enumerate_groups <- function(group) {
+  group[grepl("blank", tolower(group))] <- 0
+  group[grepl("sample", tolower(group))] <- 1
+  group[grepl("qc", tolower(group))] <- 2
+
+  return(group)
+}
+
+
+# Create appropriate input for R wavelets function
+get_wf <- function(wavelet_filter, wavelet_length) {
+  wf <- paste(wavelet_filter, wavelet_length, sep = "")
+
+  # exception to the wavelet function
+  if (wf == "d2") {
+    wf <- "haar"
+  }
+
+  return(wf)
+}
+
+
+# Exclude blanks from a dataframe
+exclude_group <- function(data, group) {
+  row_idx_to_exclude <- which(group %in% 0)
+  if (length(row_idx_to_exclude) > 0) {
+    data_without_blanks <- data[-c(row_idx_to_exclude), ]
+    cat("Blank samples have been excluded from the dataframe.\n")
+    return(data_without_blanks)
+  } else {
+    return(data)
+  }
+}
+
+
+# Store output of WaveICA in a tsv file
+store_data <- function(data, output) {
+  write.table(data, file = output, sep = "\t", row.names = FALSE, quote = FALSE)
+  cat("Normalization has been completed.\n")
+}