Merge FTIRtools into PlotFTIR

DESCRIPTION

@@ -10,15 +10,16 @@ Authors@R: c(
     person("His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources",
            role = 'cph')      
     )
-Description: The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions.
-    L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
+Description: The goal of 'PlotFTIR' is to easily and quickly kick-start the analysis and production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions.
+    L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement l'analyse et la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
 Imports: 
     cli,
     rlang,
-    scales
+    scales,
+    signal
 RoxygenNote: 7.3.2
 Depends: 
     R (>= 3.3)
@@ -33,7 +34,8 @@ Suggests:
     ir,
     ChemoSpec,
     R.utils,
-    readJDX
+    readJDX,
+    baseline
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 BugReports: https://github.com/NRCan/PlotFTIR/issues

NAMESPACE

@@ -6,23 +6,32 @@ export(add_band)
 export(add_scalar_value)
 export(add_wavenumber_marker)
 export(average_spectra)
+export(baseline_ftir)
 export(check_ftir_data)
 export(chemospec_to_plotftir)
 export(compress_low_energy)
+export(find_ftir_peaks)
+export(fit_peak_df)
+export(fit_peaks)
 export(get_plot_sample_ids)
 export(highlight_sample)
 export(ir_to_plotftir)
 export(move_plot_legend)
 export(normalize_spectra)
+export(plot_components)
+export(plot_fit_ftir_peaks)
+export(plot_fit_residuals)
 export(plot_ftir)
 export(plot_ftir_stacked)
 export(plotftir_to_chemospec)
 export(plotftir_to_ir)
 export(read_ftir)
 export(read_ftir_directory)
-export(recalculate_baseline)
+export(remove_continuum_ftir)
 export(rename_plot_sample_ids)
 export(save_plot)
+export(shift_baseline)
+export(smooth_ftir)
 export(subtract_scalar_value)
 export(transmittance_to_absorbance)
 export(zoom_in_on_range)

NEWS.md

@@ -1,5 +1,7 @@
 # PlotFTIR (development version)
 
+* Merged in deconvolution and advanced smoothing and baseline functions. (#19) 
+
 # PlotFTIR 1.2.0
 
 * Patch update to expose `check_ftir_data` for downstream packages. (related to #19)

R/io.R

@@ -189,15 +189,15 @@ read_ftir_directory <- function(path, files, sample_names = NA, ...) {
     )
   }
 
-  if (!all(is.na(sample_names))) {
+  if (all(is.na(sample_names))) {
+    sample_names <- rep(NA, length(files))
+  } else {
     if (length(sample_names) != length(files)) {
       cli::cli_abort(c(
         "Error in {.fn PlotFTIR::read_ftir_directory}: If providing {.arg sample_names} the same number of names as the number of {.arg files} must be provided.",
         i = "You provided {length(sample_names)} {.arg sample_name{?s}} and {length(files)} {.arg file{?s}}"
       ))
     }
-  } else {
-    sample_names <- rep(NA, length(files))
   }
 
   ftir <- data.frame()
@@ -219,11 +219,12 @@ read_ftir_directory <- function(path, files, sample_names = NA, ...) {
           }
         }
       },
-      error = function(e)
+      error = function(e) {
         cli::cli_warn(c(
           "{e}",
           i = "{.fn PlotFTIR::read_ftir_directory} will try to continue with the next file."
         ))
+      }
     )
   }
   if (nrow(ftir) > 0) {
@@ -381,7 +382,10 @@ read_ftir_jdx <- function(path, file, sample_name = NA, ...) {
     )
   }
   if (
-    !grepl("INFRARED", toupper(metadata[grepl("DATATYPE|DATA TYPE", metadata)]))
+    !grepl(
+      "INFRARED",
+      toupper(metadata[grepl("DATATYPE|DATA TYPE", metadata)])
+    )
   ) {
     cli::cli_abort(
       c(
@@ -392,23 +396,21 @@ read_ftir_jdx <- function(path, file, sample_name = NA, ...) {
   }
 
   intensity <- NA
-  if (any(grepl("absorbance", tolower(metadata)))) {
+  if (any(grepl("absorbance", tolower(metadata), fixed = TRUE))) {
     intensity <- "absorbance"
-  } else if (any(grepl("transmittance", tolower(metadata)))) {
+  } else if (any(grepl("transmittance", tolower(metadata), fixed = TRUE))) {
     intensity <- "transmittance"
   }
 
   ir <- jdx[[4]]
   sample_name_jdx <- names(jdx[4])
   if (is.na(sample_name)) {
     sample_name <- sample_name_jdx
-  } else {
-    if (sample_name != sample_name_jdx) {
-      cli::cli_alert_warning(c(
-        'Note: provided sample name of "{sample_name}" does not match that contained in the .jdx file: "{sample_name_jdx}".',
-        i = "Will use the provided sample name."
-      ))
-    }
+  } else if (sample_name != sample_name_jdx) {
+    cli::cli_alert_warning(c(
+      'Note: provided sample name of "{sample_name}" does not match that contained in the .jdx file: "{sample_name_jdx}".',
+      i = "Will use the provided sample name."
+    ))
   }
 
   ftir_data <- data.frame(
@@ -418,7 +420,7 @@ read_ftir_jdx <- function(path, file, sample_name = NA, ...) {
 
   if (!is.na(intensity)) {
     if (intensity_type(ftir_data) != intensity) {
-      if (intensity == 'transmittance' & max(ftir_data$intensity < 1.2)) {
+      if (intensity == "transmittance" && max(ftir_data$intensity < 1.2)) {
         # It's possible to do transmittance in 0..1 scale instead of percent.
         # PlotFTIR works better with %Transmittance
         ftir_data$intensity <- ftir_data$intensity * 100
@@ -435,7 +437,7 @@ read_ftir_jdx <- function(path, file, sample_name = NA, ...) {
     intensity <- intensity_type(ftir_data)
   }
 
-  if (intensity == 'absorbance') {
+  if (intensity == "absorbance") {
     ftir_data$absorbance <- ftir_data$intensity
   } else {
     ftir_data$transmittance <- ftir_data$intensity
@@ -504,7 +506,7 @@ save_plot <- function(ftir_spectra_plot, filename, ...) {
     ))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::save_plt}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
@@ -554,7 +556,7 @@ ir_to_plotftir <- function(ir_data, what = NA) {
 
   # Param checks
 
-  if (!("ir" %in% class(ir_data))) {
+  if (!(inherits(ir_data, "ir"))) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::ir_to_plotftir}. {.arg ir_data} must be of class {.cls ir}, produced by the {.pkg ir} package. You provided {.obj_type_friendly {ir_data}}."
     )
@@ -564,7 +566,7 @@ ir_to_plotftir <- function(ir_data, what = NA) {
     what <- seq_along(ir_data$spectra)
   }
 
-  if (suppressWarnings(any(is.na(as.numeric(what))))) {
+  if (suppressWarnings(anyNA(as.numeric(what)))) {
     if (all(what %in% ir_data$id_sample)) {
       what <- which(what %in% ir_data$id_sample)
     } else {
@@ -596,7 +598,7 @@ ir_to_df <- function(ir, what) {
   }
 
   # Param checks
-  if (!("ir" %in% class(ir))) {
+  if (!(inherits(ir, "ir"))) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::ir_to_df}. {.arg ir} must be of class {.cls ir}, produced by the {.pkg ir} package. You provided {.obj_type_friendly {ir}}."
     )
@@ -620,12 +622,10 @@ ir_to_df <- function(ir, what) {
 
     if (intensity == sample_intensity) {
       ftir <- rbind(ftir, sampleir)
+    } else if (intensity == "absorbance") {
+      ftir <- rbind(ftir, transmittance_to_absorbance(sampleir))
     } else {
-      if (intensity == "absorbance") {
-        ftir <- rbind(ftir, transmittance_to_absorbance(sampleir))
-      } else {
-        ftir <- rbind(ftir, absorbance_to_transmittance(sampleir))
-      }
+      ftir <- rbind(ftir, absorbance_to_transmittance(sampleir))
     }
   }
 
@@ -905,7 +905,7 @@ chemospec_to_plotftir <- function(csdata) {
   }
 
   # Param Checks
-  if (!("Spectra" %in% class(csdata))) {
+  if (!(inherits(csdata, "Spectra"))) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::chemospec_to_plotftir}. {.arg csdata} must be of class {.cls Spectra}, produced by the {.pkg ChemoSpec} package. You provided {.obj_type_friendly {csdata}}."
     )

R/manipulations.R

@@ -46,13 +46,13 @@ zoom_in_on_range <- function(ftir_spectra_plot, zoom_range = c(1000, 1900)) {
     ))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::zoom_in_on_range}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
   }
 
-  if (!(length(zoom_range) == 2) || !all(is.numeric(zoom_range))) {
+  if (length(zoom_range) != 2 || !all(is.numeric(zoom_range))) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::zoom_in_on_range}. {.arg zoom_range} must be a numeric vector of length two."
     )
@@ -69,7 +69,7 @@ zoom_in_on_range <- function(ftir_spectra_plot, zoom_range = c(1000, 1900)) {
   }
 
   if ("transmittance" %in% colnames(data)) {
-    if ('normal' %in% attr(ftir_spectra_plot, 'spectra_style')) {
+    if ("normal" %in% attr(ftir_spectra_plot, "spectra_style")) {
       yrange <- c(0, 100)
     } else {
       yrange <- c(0, max(c(data$transmittance, 100), na.rm = TRUE))
@@ -160,7 +160,7 @@ compress_trans <- function(intercept = 2000, ratio = 5) {
       i = "Did you accidentally put {.code -} on a new line?"
     ))
   }
-  if (!ggplot2::is.ggplot(plot)) {
+  if (!ggplot2::is_ggplot(plot)) {
     cli::cli_abort(
       "You need to have a ggplot on the left side. You provided {.obj_type_friendly { plot }}."
     )
@@ -228,7 +228,7 @@ compress_low_energy <- function(
     ))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::compress_low_energy}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
@@ -397,7 +397,7 @@ add_wavenumber_marker <- function(
     text <- as.character(as.integer(wavenumber))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::add_wavenumber_marker}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
@@ -484,7 +484,7 @@ rename_plot_sample_ids <- function(ftir_spectra_plot, sample_ids) {
     ))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::rename_plot_sample_ids}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
@@ -608,7 +608,7 @@ move_plot_legend <- function(
       i = "Install {.pkg ggplot2} with {.run install.packages('ggplot2')}"
     ))
   }
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::move_plot_legend}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
@@ -708,7 +708,7 @@ highlight_sample <- function(ftir_spectra_plot, sample_ids, ...) {
     ))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::highlight_sample}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
@@ -803,7 +803,7 @@ add_band <- function(
     ))
   }
 
-  if (!ggplot2::is.ggplot(ftir_spectra_plot)) {
+  if (!ggplot2::is_ggplot(ftir_spectra_plot)) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::add_band}. {.arg ftir_spectra_plot} must be a ggplot object. You provided {.obj_type_friendly {ftir_spectra_plot}}."
     )
@@ -827,7 +827,7 @@ add_band <- function(
     text <- ""
   }
 
-  if (!(length(wavenumber_range) == 2) || !all(is.numeric(wavenumber_range))) {
+  if (length(wavenumber_range) != 2 || !all(is.numeric(wavenumber_range))) {
     cli::cli_abort(
       "Error in {.fn PlotFTIR::add_band}. {.arg wavenumber_range} must be a numeric vector of length two."
     )