29881716206

Committed 22 Jul 2026 12:55AM UTC coverage: 97.203% (-1.0%) from 98.238%

Build # 29881716206

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Pull #36

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web-flow

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Merge 7b3b2ed32 into 8831c26fc

Pull Request Pull Request #36: Add Peak Detection and Deconvolution

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/R/plot_ftir.R

# Plot FTIR Spectra

#' PlotFTIR core plot generator
#'
#' @description Plot the FTIR spectra in a journal prepared format. Call
#'   [plot_ftir()] for basic (overlaid) plots and [plot_ftir_stacked()] for
#'   stacked and offset plots.
#'
#'   Tracez les spectres IRTF dans un format préparé par un journal. Appelez
#'   [plot_ftir()] pour les tracés de base (superposés) et [plot_ftir_stacked()]
#'   pour les tracés empilés et décalés.
#'
#' @inheritParams .shared-params
#'
#' @param ftir A data.frame in long format with columns `sample_id`,
#'   `wavenumber`, and `absorbance`. The `absorbance` column may be replaced by
#'   a `transmittance` column for transmittance plots. The code determines the
#'   correct y axis units and labels the plot/adjusts the margins appropriately.
#'
#'   Un data.frame au format long avec les colonnes `sample_id`, `wavenumber`,
#'   et `absorbance`. La colonne `absorbance` peut être remplacée par une
#'   colonne `transmittance` pour les tracés de transmission. Le code détermine
#'   les unités correctes de l'axe y et étiquette le tracé/ajuste les marges de
#'   manière appropriée.
#'
#' @keywords internal
#'
#' @return a ggplot object containing a  FTIR spectral plot. The plot and legend
#'   titles are as provided, with each sample provided a different default
#'   color. Because this is a ggplot object, any other ggplot modifiers, layers,
#'   or changes can be applied to the returned object. Further manipulations can
#'   be performed by this package. Peut également fournir `en`, `english` ou
#'   `anglais`.
#'
#'   un objet ggplot contenant un tracé spectral IRTF. Les titres de le tracé et
#'   de la légende sont tels que fournis, avec une couleur par défaut différente
#'   pour chaque échantillon. Puisqu'il s'agit d'un objet ggplot, tous les
#'   autres modificateurs, calques ou changements ggplot peuvent être appliqués
#'   à l'objet retourné. D'autres manipulations peuvent être effectuées par ce
#'   package.
#'
#' @seealso [zoom_in_on_range()] to 'zoom' into a specified range,
#'   [compress_low_energy()] to make the x axis non-linear (compressing lower
#'   energy regions), [add_wavenumber_marker()] to add markers to highlight
#'   important wavenumbers, and [move_plot_legend()] to modify the legend
#'   position.
#'
#'   [zoom_in_on_range()] pour 'zoomer' sur une gamme spécifiée,
#'   [compress_low_energy()] pour rendre l'axe x non linéaire (en compression
#'   les régions à basse énergie), [add_wavenumber_marker()] pour ajouter des
#'   marqueurs afin de mettre en évidence les nombres d'ondes importants, et
#'   [move_plot_legend()] pour modifier la position de la légende.
#'
plot_ftir_core <- function(
  ftir,
  plot_title = "FTIR Spectra",
  legend_title = "Sample ID",
  lang = NA
) {
  # Package Checks
  if (!requireNamespace("ggplot2", quietly = TRUE)) {
    cli::cli_abort(c(
      "{.pkg PlotFTIR} requires {.pkg ggplot2} package installation.",
      i = "Install {.pkg ggplot2} with {.run install.packages('ggplot2')}"
    ))
  }

  if (!requireNamespace("scales", quietly = TRUE)) {
    cli::cli_abort(c(
      "{.pkg PlotFTIR} requires {.pkg scales} package installation.",
      i = "Install {.pkg scales} with {.run install.packages('scales')}"
    ))
  }

  ftir <- check_ftir_data(ftir)
  if (!is.character(plot_title) || length(plot_title) > 2) {
    cli::cli_abort(
      "Error in {.fn PlotFTIR:::plot_ftir_core}. {.arg plot_title} must be a character string or vector of strings with length not more than two."
    )
  }
  if (!is.character(legend_title) || length(legend_title) > 1) {
    cli::cli_abort(
      "Error in {.fn PlotFTIR:::plot_ftir_core}. {.arg legend_title} must be a single character string."
    )
  }
  if (length(unique(ftir$sample_id)) > 12) {
    cli::cli_warn(c(
      "Warning in {.fn PlotFTIR:::plot_ftir_core}. The color palette in use works best with 12 or fewer unique samples in {.arg ftir}.",
      i = "You have a total of {length(unique(ftir$sample_id))} unique sample IDs."
    ))
  }

  # if language is provided, check against permitted, else use default from options
  if (!is.na(lang)) {
    lang <- rlang::arg_match(
      lang,
      values = c(
        "en",
        "english",
        "anglais",
        "fr",
        "french",
        "francais",
        "fran\u00e7ais"
      ),
      multiple = FALSE
    )
  } else {
    lang <- getOption("PlotFTIR.lang", default = "en")
  }

  l <- substr(lang, 0, 2)
  if (l == "fr") {
    if (all(plot_title == "FTIR Spectra")) {
      plot_title <- "Spectres IRTF"
    }
    if (legend_title == "Sample ID") {
      legend_title <- "ID de l'\u00e9chantillon"
    }
  }

  mode <- attr(ftir, "intensity")

  if (l == "fr") {
    xtitle <- bquote("Nombre d'onde" ~ (cm^-1))
  } else {
    xtitle <- bquote("Wavenumber" ~ (cm^-1))
  }

  ytitle <- ifelse(
    mode %in% c("absorbance", "normalized absorbance"),
    "Absorbance",
    "% Transmittance"
  )

  if (grepl("normalized", mode)) {
    ytitle <- paste("Normalized", ytitle)
  }

  ftir <- ftir[stats::complete.cases(ftir), ]
  ftir$wavenumber <- as.numeric(ftir$wavenumber)

  if (grepl("absorbance", mode)) {
    ftir$absorbance <- as.numeric(ftir$absorbance)
    p <- ggplot2::ggplot(ftir) +
      ggplot2::geom_line(ggplot2::aes(
        x = .data$wavenumber,
        y = .data$absorbance,
        color = as.factor(.data$sample_id)
      )) +
      ggplot2::scale_y_continuous()
  } else {
    ftir$transmittance <- as.numeric(ftir$transmittance)
    p <- ggplot2::ggplot(ftir) +
      ggplot2::geom_line(ggplot2::aes(
        x = .data$wavenumber,
        y = .data$transmittance,
        color = as.factor(.data$sample_id)
      )) +
      ggplot2::scale_y_continuous(breaks = scales::breaks_width(20)) +
      ggplot2::coord_cartesian(ylim = c(0, 100))
  }

  p <- p +
    ggplot2::labs(
      title = plot_title[1],
      subtitle = if (length(plot_title) < 2) NULL else plot_title[2], # Can't return Null from ifelse()
      x = xtitle,
      y = ytitle
    ) +
    ggplot2::guides(
      color = ggplot2::guide_legend(title = legend_title),
      x = ggplot2::guide_axis(minor.ticks = TRUE)
    ) +
    ggplot2::theme_light() +
    ggplot2::scale_x_reverse(
      breaks = scales::breaks_extended(),
      expand = ggplot2::expansion()
    )

  if (
    !requireNamespace("ggthemes", quietly = TRUE) ||
      length(unique(ftir$sample_id)) > 15
  ) {
    p <- p +
      ggplot2::scale_color_viridis_d()
  } else {
    p <- p +
      ggthemes::scale_color_calc()
  }

  if (grepl("normalized", mode)) {
    p <- p +
      ggplot2::theme(
        axis.text.y = ggplot2::element_blank()
      )
  }

  attr(p, "intensity") <- attr(ftir, "intensity")

  return(p)
}


#' Plot FTIR in stacked format
#'
#' @description Plot the FTIR spectra in a journal prepared format. It may be
#'  desirable to plot spectra 'stacked and offset' by a certain amount. In this
#'  case the y axis becomes non-labelled and each charts baseline (0 for
#'  absorbance or 100 for transmittance) is offset by a certain amount.
#'
#'  Tracez les spectres IRTF dans un format préparé par un journal. Il peut être
#'  souhaitable de tracer les spectres 'empilés et décalés' d'une
#'  certaine quantité. Dans ce cas l'axe y devient non étiqueté et
#'  chaque ligne de base du graphique (0 pour absorbance ou 100 pour la
#'  transmittance) est décalée d'une certaine quantité.
#'
#' @inheritParams plot_ftir_core
#' @param stack_offset The amount in percentage of stacking offset to use. For
#'  transmittance this is directly linked to the units of Y axis, for absorbance
#'  this is about 0.2 absorbance units.
#'
#'  Le montant en pourcentage de décalage d'empilement à utiliser. Pour
#'  transmittance, cette valeur est directement liée aux unités de l'axe y, pour
#'  l'absorbance cela représente environ 0,2 unités d'absorbance.
#'
#' @inherit plot_ftir_core return
#'
#' @inherit plot_ftir_core seealso
#' @export
#'
#' @examples
#' if (requireNamespace("ggplot2", quietly = TRUE)) {
#'   # Plot FTIR spectras stacked showing the differences in the `biodiesel` dataset
#'   plot_ftir_stacked(biodiesel)
#' }
plot_ftir_stacked <- function(
  ftir,
  plot_title = "FTIR Spectra",
  legend_title = "Sample ID",
  stack_offset = 10,
  lang = NA
) {
  ftir <- check_ftir_data(ftir)

  if (!is.numeric(stack_offset) || length(stack_offset) > 1) {
    cli::cli_abort(
      "Error in {.fn PlotFTIR:::plot_ftir_stacked}. {.arg stack_offset} must be a single numeric value."
    )
  }
  if (stack_offset < 0 || stack_offset > 200) {
    cli::cli_abort(
      "Error in {.fn PlotFTIR:::plot_ftir_stacked}. {.arg stack_offset} must be between 0 and 200."
    )
  }

  mode <- attr(ftir, "intensity")

  # Stack FTIR traces by 10% of range number of unique samples
  stack_samples <- unique(ftir$sample_id)
  nsamples <- length(unique(stack_samples))

  if (nsamples > 1) {
    if (grepl("absorbance", mode)) {
      # Transmittance gets an offset of stack_offset % against a percentage scale
      # for absorbance, most signals max out around 2 so that's the range.
      stack_offset <- (stack_offset / 100) * 2.0
    }
    offset <- data.frame(
      "sample_id" = stack_samples,
      "offset" = seq(from = 0, by = stack_offset, length.out = nsamples)
    )

    ftir <- merge(x = ftir, y = offset, by = "sample_id")
    if (grepl("absorbance", mode)) {
      ftir$absorbance <- ftir$absorbance + ftir$offset
    } else {
      ftir$transmittance <- ftir$transmittance + ftir$offset
    }
    ftir$offset <- NULL
  }

  p <- plot_ftir_core(
    ftir = ftir,
    plot_title = plot_title,
    legend_title = legend_title,
    lang = lang
  )

  p <- p + ggplot2::theme(axis.text.y = ggplot2::element_blank())
  suppressMessages(p <- p + ggplot2::coord_cartesian(ylim = c(0, NA)))

  if (grepl("absorbance", mode)) {
    p <- p + ggplot2::ylab("Absorbance (a.u.)")
  } else {
    p <- p + ggplot2::ylab("Transmittance (a.u.)")
  }

  attr(p, "spectra_style") <- "stacked"

  return(p)
}


#' Plot FTIR Spectra Overlaid
#'
#' @description Produce a basic spectra overlay plot for all samples found in
#' the FTIR dataset provided.
#'
#' Produisez un tracé de base de superposition de spectres pour tous les
#' échantillons trouvés dans l'ensemble de données IRTF fourni.
#'
#' @inherit plot_ftir_core params return
#' @export
#'
#' @examples
#' if (requireNamespace("ggplot2", quietly = TRUE)) {
#'   # Plot a basic FTIR Spectra overlay from the `sample_spectra` data set with default titles
#'   plot_ftir(sample_spectra)
#' }
plot_ftir <- function(
  ftir,
  plot_title = "FTIR Spectra",
  legend_title = "Sample ID",
  lang = NA
) {
  ftir <- check_ftir_data(ftir)
  p <- plot_ftir_core(
    ftir = ftir,
    plot_title = plot_title,
    legend_title = legend_title,
    lang = lang
  )

  attr(p, "spectra_style") <- "normal"

  return(p)
}

1	# Plot FTIR Spectra
2
3	#' PlotFTIR core plot generator
4	#'
5	#' @description Plot the FTIR spectra in a journal prepared format. Call
6	#' [plot_ftir()] for basic (overlaid) plots and [plot_ftir_stacked()] for
7	#' stacked and offset plots.
8	#'
9	#' Tracez les spectres IRTF dans un format préparé par un journal. Appelez
10	#' [plot_ftir()] pour les tracés de base (superposés) et [plot_ftir_stacked()]
11	#' pour les tracés empilés et décalés.
12	#'
13	#' @inheritParams .shared-params
14	#'
15	#' @param ftir A data.frame in long format with columns `sample_id`,
16	#' `wavenumber`, and `absorbance`. The `absorbance` column may be replaced by
17	#' a `transmittance` column for transmittance plots. The code determines the
18	#' correct y axis units and labels the plot/adjusts the margins appropriately.
19	#'
20	#' Un data.frame au format long avec les colonnes `sample_id`, `wavenumber`,
21	#' et `absorbance`. La colonne `absorbance` peut être remplacée par une
22	#' colonne `transmittance` pour les tracés de transmission. Le code détermine
23	#' les unités correctes de l'axe y et étiquette le tracé/ajuste les marges de
24	#' manière appropriée.
25	#'
26	#' @keywords internal
27	#'
28	#' @return a ggplot object containing a FTIR spectral plot. The plot and legend
29	#' titles are as provided, with each sample provided a different default
30	#' color. Because this is a ggplot object, any other ggplot modifiers, layers,
31	#' or changes can be applied to the returned object. Further manipulations can
32	#' be performed by this package. Peut également fournir `en`, `english` ou
33	#' `anglais`.
34	#'
35	#' un objet ggplot contenant un tracé spectral IRTF. Les titres de le tracé et
36	#' de la légende sont tels que fournis, avec une couleur par défaut différente
37	#' pour chaque échantillon. Puisqu'il s'agit d'un objet ggplot, tous les
38	#' autres modificateurs, calques ou changements ggplot peuvent être appliqués
39	#' à l'objet retourné. D'autres manipulations peuvent être effectuées par ce
40	#' package.
41	#'
42	#' @seealso [zoom_in_on_range()] to 'zoom' into a specified range,
43	#' [compress_low_energy()] to make the x axis non-linear (compressing lower
44	#' energy regions), [add_wavenumber_marker()] to add markers to highlight
45	#' important wavenumbers, and [move_plot_legend()] to modify the legend
46	#' position.
47	#'
48	#' [zoom_in_on_range()] pour 'zoomer' sur une gamme spécifiée,
49	#' [compress_low_energy()] pour rendre l'axe x non linéaire (en compression
50	#' les régions à basse énergie), [add_wavenumber_marker()] pour ajouter des
51	#' marqueurs afin de mettre en évidence les nombres d'ondes importants, et
52	#' [move_plot_legend()] pour modifier la position de la légende.
53	#'
54	plot_ftir_core <- function(
55	ftir,
56	plot_title = "FTIR Spectra",
57	legend_title = "Sample ID",
58	lang = NA
59	) {
60	# Package Checks
61	if (!requireNamespace("ggplot2", quietly = TRUE)) {	78✔
62	cli::cli_abort(c(	1✔
63	"{.pkg PlotFTIR} requires {.pkg ggplot2} package installation.",	1✔
64	i = "Install {.pkg ggplot2} with {.run install.packages('ggplot2')}"	1✔
65	))	1✔
66	}
67
68	if (!requireNamespace("scales", quietly = TRUE)) {	77✔
NEW 69	cli::cli_abort(c(	×
NEW 70	"{.pkg PlotFTIR} requires {.pkg scales} package installation.",	×
NEW 71	i = "Install {.pkg scales} with {.run install.packages('scales')}"	×
NEW 72	))	×
73	}
74
75	ftir <- check_ftir_data(ftir)	77✔
76	if (!is.character(plot_title) \|\| length(plot_title) > 2) {	77✔
77	cli::cli_abort(	4✔
78	"Error in {.fn PlotFTIR:::plot_ftir_core}. {.arg plot_title} must be a character string or vector of strings with length not more than two."	4✔
79	)	4✔
80	}
81	if (!is.character(legend_title) \|\| length(legend_title) > 1) {	73✔
82	cli::cli_abort(	2✔
83	"Error in {.fn PlotFTIR:::plot_ftir_core}. {.arg legend_title} must be a single character string."	2✔
84	)	2✔
85	}
86	if (length(unique(ftir$sample_id)) > 12) {	71✔
87	cli::cli_warn(c(	17✔
88	"Warning in {.fn PlotFTIR:::plot_ftir_core}. The color palette in use works best with 12 or fewer unique samples in {.arg ftir}.",	17✔
89	i = "You have a total of {length(unique(ftir$sample_id))} unique sample IDs."	17✔
90	))	17✔
91	}
92
93	# if language is provided, check against permitted, else use default from options
94	if (!is.na(lang)) {	71✔
95	lang <- rlang::arg_match(	31✔
96	lang,	31✔
97	values = c(	31✔
98	"en",	31✔
99	"english",	31✔
100	"anglais",	31✔
101	"fr",	31✔
102	"french",	31✔
103	"francais",	31✔
104	"fran\u00e7ais"	31✔
105	),	31✔
106	multiple = FALSE	31✔
107	)	31✔
108	} else {
109	lang <- getOption("PlotFTIR.lang", default = "en")	40✔
110	}
111
112	l <- substr(lang, 0, 2)	67✔
113	if (l == "fr") {	67✔
114	if (all(plot_title == "FTIR Spectra")) {	8✔
115	plot_title <- "Spectres IRTF"	2✔
116	}
117	if (legend_title == "Sample ID") {	8✔
118	legend_title <- "ID de l'\u00e9chantillon"	4✔
119	}
120	}
121
122	mode <- attr(ftir, "intensity")	67✔
123
124	if (l == "fr") {	67✔
125	xtitle <- bquote("Nombre d'onde" ~ (cm^-1))	8✔
126	} else {
127	xtitle <- bquote("Wavenumber" ~ (cm^-1))	59✔
128	}
129
130	ytitle <- ifelse(	67✔
131	mode %in% c("absorbance", "normalized absorbance"),	67✔
132	"Absorbance",	67✔
133	"% Transmittance"	67✔
134	)	67✔
135
136	if (grepl("normalized", mode)) {	67✔
137	ytitle <- paste("Normalized", ytitle)	2✔
138	}
139
140	ftir <- ftir[stats::complete.cases(ftir), ]	67✔
141	ftir$wavenumber <- as.numeric(ftir$wavenumber)	67✔
142
143	if (grepl("absorbance", mode)) {	67✔
144	ftir$absorbance <- as.numeric(ftir$absorbance)	59✔
145	p <- ggplot2::ggplot(ftir) +	59✔
146	ggplot2::geom_line(ggplot2::aes(	59✔
147	x = .data$wavenumber,	59✔
148	y = .data$absorbance,	59✔
149	color = as.factor(.data$sample_id)	59✔
150	)) +	59✔
151	ggplot2::scale_y_continuous()	59✔
152	} else {
153	ftir$transmittance <- as.numeric(ftir$transmittance)	8✔
154	p <- ggplot2::ggplot(ftir) +	8✔
155	ggplot2::geom_line(ggplot2::aes(	8✔
156	x = .data$wavenumber,	8✔
157	y = .data$transmittance,	8✔
158	color = as.factor(.data$sample_id)	8✔
159	)) +	8✔
160	ggplot2::scale_y_continuous(breaks = scales::breaks_width(20)) +	8✔
161	ggplot2::coord_cartesian(ylim = c(0, 100))	8✔
162	}
163
164	p <- p +	67✔
165	ggplot2::labs(	67✔
166	title = plot_title[1],	67✔
167	subtitle = if (length(plot_title) < 2) NULL else plot_title[2], # Can't return Null from ifelse()	67✔
168	x = xtitle,	67✔
169	y = ytitle	67✔
170	) +	67✔
171	ggplot2::guides(	67✔
172	color = ggplot2::guide_legend(title = legend_title),	67✔
173	x = ggplot2::guide_axis(minor.ticks = TRUE)	67✔
174	) +	67✔
175	ggplot2::theme_light() +	67✔
176	ggplot2::scale_x_reverse(	67✔
177	breaks = scales::breaks_extended(),	67✔
178	expand = ggplot2::expansion()	67✔
179	)	67✔
180
181	if (
182	!requireNamespace("ggthemes", quietly = TRUE) \|\|	67✔
183	length(unique(ftir$sample_id)) > 15	67✔
184	) {
185	p <- p +	36✔
186	ggplot2::scale_color_viridis_d()	36✔
187	} else {
188	p <- p +	31✔
189	ggthemes::scale_color_calc()	31✔
190	}
191
192	if (grepl("normalized", mode)) {	67✔
193	p <- p +	2✔
194	ggplot2::theme(	2✔
195	axis.text.y = ggplot2::element_blank()	2✔
196	)	2✔
197	}
198
199	attr(p, "intensity") <- attr(ftir, "intensity")	67✔
200
201	return(p)	67✔
202	}
203
204
205	#' Plot FTIR in stacked format
206	#'
207	#' @description Plot the FTIR spectra in a journal prepared format. It may be
208	#' desirable to plot spectra 'stacked and offset' by a certain amount. In this
209	#' case the y axis becomes non-labelled and each charts baseline (0 for
210	#' absorbance or 100 for transmittance) is offset by a certain amount.
211	#'
212	#' Tracez les spectres IRTF dans un format préparé par un journal. Il peut être
213	#' souhaitable de tracer les spectres 'empilés et décalés' d'une
214	#' certaine quantité. Dans ce cas l'axe y devient non étiqueté et
215	#' chaque ligne de base du graphique (0 pour absorbance ou 100 pour la
216	#' transmittance) est décalée d'une certaine quantité.
217	#'
218	#' @inheritParams plot_ftir_core
219	#' @param stack_offset The amount in percentage of stacking offset to use. For
220	#' transmittance this is directly linked to the units of Y axis, for absorbance
221	#' this is about 0.2 absorbance units.
222	#'
223	#' Le montant en pourcentage de décalage d'empilement à utiliser. Pour
224	#' transmittance, cette valeur est directement liée aux unités de l'axe y, pour
225	#' l'absorbance cela représente environ 0,2 unités d'absorbance.
226	#'
227	#' @inherit plot_ftir_core return
228	#'
229	#' @inherit plot_ftir_core seealso
230	#' @export
231	#'
232	#' @examples
233	#' if (requireNamespace("ggplot2", quietly = TRUE)) {
234	#' # Plot FTIR spectras stacked showing the differences in the `biodiesel` dataset
235	#' plot_ftir_stacked(biodiesel)
236	#' }
237	plot_ftir_stacked <- function(
238	ftir,
239	plot_title = "FTIR Spectra",
240	legend_title = "Sample ID",
241	stack_offset = 10,
242	lang = NA
243	) {
244	ftir <- check_ftir_data(ftir)	22✔
245
246	if (!is.numeric(stack_offset) \|\| length(stack_offset) > 1) {	12✔
247	cli::cli_abort(	2✔
248	"Error in {.fn PlotFTIR:::plot_ftir_stacked}. {.arg stack_offset} must be a single numeric value."	2✔
249	)	2✔
250	}
251	if (stack_offset < 0 \|\| stack_offset > 200) {	10✔
252	cli::cli_abort(	2✔
253	"Error in {.fn PlotFTIR:::plot_ftir_stacked}. {.arg stack_offset} must be between 0 and 200."	2✔
254	)	2✔
255	}
256
257	mode <- attr(ftir, "intensity")	8✔
258
259	# Stack FTIR traces by 10% of range number of unique samples
260	stack_samples <- unique(ftir$sample_id)	8✔
261	nsamples <- length(unique(stack_samples))	8✔
262
263	if (nsamples > 1) {	8✔
264	if (grepl("absorbance", mode)) {	8✔
265	# Transmittance gets an offset of stack_offset % against a percentage scale
266	# for absorbance, most signals max out around 2 so that's the range.
267	stack_offset <- (stack_offset / 100) * 2.0	4✔
268	}
269	offset <- data.frame(	8✔
270	"sample_id" = stack_samples,	8✔
271	"offset" = seq(from = 0, by = stack_offset, length.out = nsamples)	8✔
272	)	8✔
273
274	ftir <- merge(x = ftir, y = offset, by = "sample_id")	8✔
275	if (grepl("absorbance", mode)) {	8✔
276	ftir$absorbance <- ftir$absorbance + ftir$offset	4✔
277	} else {
278	ftir$transmittance <- ftir$transmittance + ftir$offset	4✔
279	}
280	ftir$offset <- NULL	8✔
281	}
282
283	p <- plot_ftir_core(	8✔
284	ftir = ftir,	8✔
285	plot_title = plot_title,	8✔
286	legend_title = legend_title,	8✔
287	lang = lang	8✔
288	)	8✔
289
290	p <- p + ggplot2::theme(axis.text.y = ggplot2::element_blank())	6✔
291	suppressMessages(p <- p + ggplot2::coord_cartesian(ylim = c(0, NA)))	6✔
292
293	if (grepl("absorbance", mode)) {	6✔
294	p <- p + ggplot2::ylab("Absorbance (a.u.)")	2✔
295	} else {
296	p <- p + ggplot2::ylab("Transmittance (a.u.)")	4✔
297	}
298
299	attr(p, "spectra_style") <- "stacked"	6✔
300
301	return(p)	6✔
302	}
303
304
305	#' Plot FTIR Spectra Overlaid
306	#'
307	#' @description Produce a basic spectra overlay plot for all samples found in
308	#' the FTIR dataset provided.
309	#'
310	#' Produisez un tracé de base de superposition de spectres pour tous les
311	#' échantillons trouvés dans l'ensemble de données IRTF fourni.
312	#'
313	#' @inherit plot_ftir_core params return
314	#' @export
315	#'
316	#' @examples
317	#' if (requireNamespace("ggplot2", quietly = TRUE)) {
318	#' # Plot a basic FTIR Spectra overlay from the `sample_spectra` data set with default titles
319	#' plot_ftir(sample_spectra)
320	#' }
321	plot_ftir <- function(
322	ftir,
323	plot_title = "FTIR Spectra",
324	legend_title = "Sample ID",
325	lang = NA
326	) {
327	ftir <- check_ftir_data(ftir)	80✔
328	p <- plot_ftir_core(	70✔
329	ftir = ftir,	70✔
330	plot_title = plot_title,	70✔
331	legend_title = legend_title,	70✔
332	lang = lang	70✔
333	)	70✔
334
335	attr(p, "spectra_style") <- "normal"	61✔
336
337	return(p)	61✔
338	}

NRCan / PlotFTIR / 29881716206

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