introduce plotting

R/extract_metadata.R

@@ -16,7 +16,7 @@ get_basic_metadata <- function(ds_list) {
 
 get_meta_timestamp <- function(ds_list) {
   text <- ds_list$history$text
-  history <- paste0(text, collapse = "") 
+  history <- paste0(text, collapse = "")
   save_file_time <- gsub(".*Save File\t\t(\\d.*)\t\t\t.*", "\\1", history)
 
   time_hour_tz <- strsplit(x = save_file_time, split = " ")[[1L]]
@@ -41,7 +41,7 @@ get_meta_timestamp <- function(ds_list) {
 get_meta_utc_datetime <- function(timestamp) {
   tz <- timestamp$timezone
   utc_diff <- as.integer(gsub("\\D+(\\+\\d)", "\\1", tz))
-  utc_datetime <-  as.POSIXct(strptime(timestamp$datetime,
+  utc_datetime <- as.POSIXct(strptime(timestamp$datetime,
     format = "%Y-%m-%d %H:%M:%S",
     tz = "UTC"
   )) - (utc_diff * 3600)

plot.R

@@ -0,0 +1,87 @@
+#' Plot spectra read from OPUS files
+#'
+#' @param data list of class "opusreader2" (single OPUS file) or both
+#' "opusreader2" and "list_opusreader2", containing spectral data parsed from
+#' Bruker OPUS binary files.
+#' @param data_type character vector of length one with desired spectral data
+#' type to plot.
+#' @param plot_type plot type, either `"base"``, printing a base plot, or
+#' `"ggplot2"``, which returns a ggplot2 object.
+#' @family core
+#' @return a base R plot with spectra
+#'
+#' @export
+plot <- function(data,
+                 data_type = c(
+                   "ref_no_atm_comp", "refl",
+                   "ab_no_atm_comp", "ab",
+                   "sc_sample", "ig_sample",
+                   "sc_ref", "ig_ref"
+                 ),
+                 plot_type = c("base", "ggplot2")) {
+  UseMethod("plot")
+}
+
+
+plot.opusreader2 <- function(data, data_type, plot_type) {
+  data_type <- match.arg(data_type)
+  plot_type <- match.arg(plot_type)
+
+  validate_plot(data, data_type, plot_type)
+
+  # get the spectra (y) and x (x-axis; e.g. wavenumber)
+  if (inherits(data, "list_opusreader2")) {
+    spectra <- do.call(
+      rbind,
+      Map(function(x) x[[y]], x = data, y = data_type)
+    )
+  } else {
+    spectra <- data[[data_type]]
+  }
+
+  ylab <- switch(
+    EXPR = data_type,
+    "ref_no_atm_comp" = "Reflectance (no atm. comp.)",
+    "refl" = "Reflectance",
+    "ab_no_atm_comp" = "Absorbance (no atm. comp.)",
+    "ab" = "Absorbance",
+    "sc_sample" = "Single channel sample",
+    "ig_sample" = "Interferogram sample",
+    "sc_ref" = "Single channel reference",
+    "ig_ref" = "Interferogram sample"
+  )
+
+  matplot(
+    x = x,
+    y = t(spectra),
+    type = "l",
+    lwd = 1.5,
+    xlab = xlab,
+    ylab = ylab
+  )
+}
+
+validate_plot <- function(data, data_type, plot_type) {
+  stopifnot(
+    inherits(data, "opusreader2")
+  )
+  validate_plot_data_type(data, data_type)
+}
+
+validate_plot_data_type <- function(data, data_type, plot_type) {
+  if (inherits(data, "list_opusreader2")) {
+    all_data_types <- all(
+      unlist(lapply(data, function(x) data_type %in% names(x)))
+    )
+  } else {
+    all_data_types <- data_type %in% names(data)
+  }
+
+  if (!isTRUE(all_data_types)) {
+    stop("All `data` elements need to contain `data_type`",
+      paste0(data_type, "."),
+      call. = FALSE
+    )
+  }
+  invisible(all_data_types)
+}

vignettes/introduction.Rmd

@@ -50,4 +50,4 @@ For single OPUS files, there is also a lower level implementation.
 
 ```r
 data_single <- read_opus_single(dsn = file)
-```
+```