Nothing
R/plot_NMR.R
In SOMnmR: Analysis of Soil Organic Matter using Nuclear Magnetic Resonance
#' NMR Plotting Function
#'
#' This function allows you to plot the 13C-NMR spectra using marking different integration regions.
#' The loaded Raw spectra are intensity normalized and plotted with the chosen integration regions, either spinning side bands (default),
#' the Bonanomi("Bonanomi") regions or the Molecular Mixing Model regions("MMM").
#' The function returns the plots as images either tiff or png, normalized and flattened spectrum
#' @param raw.spec loaded NMR spectra
#' @param NMRmeth Regions to be integrated, methods available include: "4region", "Bonanomi", "Smernik" and Molecular mixing model ("MMM").
#' @param use.tiff Logical, default to FALSE (use png)
#' @param set.plot.ymax Set maximum of plot y axis, defaults to NULL
#' @param file.output Logical, default to FALSE
#' @returns A plot of the NMR spectrum and a csv file of the data plotted.
#' @keywords normalization integration
#' @export
#' @import ggplot2
#' @examples
#' \donttest{
#' library(ggplot2)
#' data("GarciaF200")
#' plot_NMR(GarciaF200, NMRmeth = "MMM", file.output = FALSE, use.tiff = FALSE)
#' }
plot_NMR <- function (raw.spec, NMRmeth = NULL, use.tiff = NULL,
set.plot.ymax = NULL, file.output = NULL) {
## check and assign FALSE if optional parameters are not set
if(is.null(use.tiff)) {use.tiff <- FALSE}
if(is.null(file.output)) {file.output <- FALSE}
for (i in 1:length(raw.spec)) {
sample.name <- raw.spec[[i]]$name
corr.spec <- raw.spec[[i]]$data$raw.spec
corr.spec$raw.intensity <- (corr.spec$raw.intensity/max(corr.spec$raw.intensity))*100
## create list of new sample for fitting function
new.spec <- list("name" = raw.spec[[i]]$name, "data" = list("corr.spec" = corr.spec))
ppm <- NULL
norm.intensity <- NULL
if (file.output == TRUE) {
output.spec <- data.frame(cbind(ppm = corr.spec$ppm, norm.intensity = corr.spec$raw.intensity))
write.csv2(output.spec, paste("output.", sample.name, "csv", sep = "."), row.names = FALSE)
} else if (file.output == FALSE) {
output.spec <- data.frame(cbind(ppm = corr.spec$ppm, norm.intensity = corr.spec$raw.intensity))
}
## create image file name with high resolution (png or tiff)
if (file.output == TRUE) {
if (use.tiff == TRUE) {
tiff(filename = paste(sample.name, "normalized.tiff", sep = "."),
width = 3200, height = 3200, units = "px", res = 400,
compression = c("none"))
} else {
png(filename = paste(sample.name, "normalized.png", sep = "."),
width = 3200, height = 3200, units = "px", res = 400)
}
## create header name
head.name <- paste(sample.name, "normalized", sep = " ")
} else {
## simply use sample name as header name
head.name <- paste(sample.name)
}
## preserving old parameters
oldpar <- par(no.readonly = TRUE)
# Ensure the original graphical parameters are restored on exit
on.exit(par(oldpar))
## set squared plots (pty), margins (mar), and size of plot (cex)
if (file.output == TRUE) {
par(pty="s",
mar=c(5,3,2,0)+0.1, # c(bottom, left, top, right)
cex = 0.5
)
}
if (is.null(set.plot.ymax)) {
plot.ymax <- max(output.spec$norm.intensity)+0.5
} else {
plot.ymax <- set.plot.ymax
}
if (is.null(NMRmeth)) {
raincloud_theme = theme(
text = element_text(size = 16),
axis.title.x=element_text(size = 16),
axis.title.y = element_text(size = 16),
axis.text = element_text(size = 16),
axis.text.x = element_text(angle = 0, vjust = 0.5),
legend.title=element_blank(),
legend.text=element_text(size=16),
legend.position = c(0.8,0.85),
plot.title = element_text(lineheight=.8, face="bold", size = 16),
panel.border = element_blank(),
panel.background = element_blank(),
panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
axis.line.x = element_line(colour = 'black', size=0.5, linetype='solid'),
axis.line.y = element_line(colour = 'black', size=0.5, linetype='solid'))
colors <- c("Alkyl-C" = "#CC79A7", "O/N-Alkyl-C" = "#0072B2", "Aryl-C" = "#E69F00", "Carboxyl-C" = "#009E73")
## plot the coordinate system
plt <- ggplot(data = output.spec, mapping = aes(x = ppm, y = norm.intensity)) +
scale_fill_manual(breaks = c("Alkyl-C", "O/N-Alkyl-C", "Aryl-C", "Carboxyl-C"),values=colors, labels = c("Alkyl-C", "O/N-Alkyl-C", "Aryl-C", "Carboxyl-C"))+
## area of Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm>0 & ppm< 45 , ppm, NA), fill = "Alkyl-C"), alpha = 0.8, size = 0.6) +
## area of O Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm>45 & ppm< 110 , ppm, NA), fill = "O/N-Alkyl-C"), alpha = 0.8, size = 0.6) +
## area of Aryl-C
geom_area(mapping = aes(x = ifelse(ppm>110 & ppm< 160 , ppm, NA), fill = "Aryl-C"), alpha = 0.8, size = 0.6) +
## area of carboxyl-C
geom_area(mapping = aes(x = ifelse(ppm>160 & ppm< 220 , ppm, NA), fill = "Carboxyl-C"), alpha = 0.8, size = 0.6) +
## plot the NMR spectrum
geom_line(size = 0.25)+
## Axis title
xlab("Chemical shift (ppm)") +
ylab("Intensity")+
## create line y = 0
ylim(-5, plot.ymax)+
scale_x_reverse(limits=c(400, -200))+
raincloud_theme
print(plt)
} else if (NMRmeth == "Smernik") {
raincloud_theme = theme(
text = element_text(size = 16),
axis.title.x=element_text(size = 16),
axis.title.y = element_text(size = 16),
axis.text = element_text(size = 16),
axis.text.x = element_text(angle = 0, vjust = 0.5),
legend.title=element_blank(),
legend.text=element_text(size=16),
legend.position = c(0.8,0.85),
plot.title = element_text(lineheight=.8, face="bold", size = 16),
panel.border = element_blank(),
panel.background = element_blank(),
panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
axis.line.x = element_line(colour = 'black', size=0.5, linetype='solid'),
axis.line.y = element_line(colour = 'black', size=0.5, linetype='solid'))
colors <- c("Alkyl-C" = "#CC79A7", "O/N-Alkyl-C" = "#0072B2", "Aryl-C" = "#E69F00", "Carboxyl-C" = "#009E73")
## plot the coordinate system
plt <- ggplot(data = output.spec, mapping = aes(x = ppm, y = norm.intensity)) +
scale_fill_manual(breaks = c("Alkyl-C", "O/N-Alkyl-C", "Aryl-C", "Carboxyl-C"),values=colors, labels = c("Alkyl-C", "O/N-Alkyl-C", "Aryl-C", "Carboxyl-C"))+
## area of Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm>0 & ppm< 45 , ppm, NA), fill = "Alkyl-C"), alpha = 0.8, size = 0.6) +
## area of O Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm>45 & ppm< 110 , ppm, NA), fill = "O/N-Alkyl-C"), alpha = 0.8, size = 0.6) +
## area of Aryl-C
geom_area(mapping = aes(x = ifelse(ppm>110 & ppm< 165 , ppm, NA), fill = "Aryl-C"), alpha = 0.8, size = 0.6) +
## area of carboxyl-C
geom_area(mapping = aes(x = ifelse(ppm>165 & ppm< 185 , ppm, NA), fill = "Carboxyl-C"), alpha = 0.8, size = 0.6) +
## plot the NMR spectrum
geom_line(size = 0.25)+
## Axis title
xlab("Chemical shift (ppm)") +
ylab("Intensity")+
## create line y = 0
ylim(-5, plot.ymax)+
scale_x_reverse(limits=c(400, -200))+
raincloud_theme
print(plt)
} else if (NMRmeth == "Bonanomi") {
raincloud_theme = theme(
text = element_text(size = 16),
axis.title.x=element_text(size = 16),
axis.title.y = element_text(size = 16),
axis.text = element_text(size = 16),
axis.text.x = element_text(angle = 0, vjust = 0.5),
legend.title=element_blank(),
legend.text=element_text(size=16),
legend.position = c(0.8,0.85),
plot.title = element_text(lineheight=.8, face="bold", size = 16),
panel.border = element_blank(),
panel.background = element_blank(),
panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
axis.line.x = element_line(colour = 'black', size=0.5, linetype='solid'),
axis.line.y = element_line(colour = 'black', size=0.5, linetype='solid'))
colors <- c("Alkyl-C" = "#CC79A7", "Methoxyl/N-Alkyl-C"= "#D55E00", "O-Alkyl-C" = "#0072B2", "Di-O-Alkyl-C" = "#F0E442",
"Aromatic-C" = "#56B4E9", "Phenolic-C" = "#E69F00", "Carbonyl and amide-C" = "#999999", "Ketone-C" = "#009E73")
## plot the coordinate system
plt <- ggplot(data = output.spec, mapping = aes(x = ppm, y = norm.intensity)) +
scale_fill_manual(breaks = c("Alkyl-C", "Methoxyl/N-Alkyl-C", "O-Alkyl-C", "Di-O-Alkyl-C", "Aromatic-C",
"Phenolic-C", "Carbonyl and amide-C", "Ketone-C"),
values=colors,
labels = c("Alkyl-C", "Methoxyl/N-Alkyl-C", "O-Alkyl-C", "Di-O-Alkyl-C", "Aromatic-C",
"Phenolic-C", "Carbonyl and amide-C","Ketone-C"))+
## area of Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm >= 0 & ppm <= 45, ppm,NA), y = norm.intensity, fill = "Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of Methoxyl-C
geom_area(mapping = aes(x = ifelse(ppm> 46 & ppm< 60 , ppm, NA), y = norm.intensity, fill = "Methoxyl/N-Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of O-Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm> 61 & ppm< 90 , ppm, NA), y = norm.intensity, fill = "O-Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of Di-O-Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm> 91 & ppm< 110 , ppm, NA), y = norm.intensity, fill = "Di-O-Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of H and C substituted aromatic -C
geom_area(mapping = aes(x = ifelse(ppm> 111 & ppm< 140 , ppm, NA), y = norm.intensity, fill = "Aromatic-C"), alpha = 0.8, size = 0.5) +
## area of O substituted aromatic -C
geom_area(mapping = aes(x = ifelse(ppm> 141 & ppm< 160 , ppm, NA), y = norm.intensity, fill = "Phenolic-C"), alpha = 0.8, size = 0.5) +
## area of carboxyl-C
geom_area(mapping = aes(x = ifelse(ppm> 161 & ppm< 190 , ppm, NA), y = norm.intensity, fill = "Carbonyl and amide-C"), alpha = 0.8, size = 0.5) +
## plot the NMR spectrum
geom_line(size = 0.25)+
## Axis title
xlab("Chemical shift (ppm)") +
ylab("Intensity")+
## create line y = 0
ylim(-5, plot.ymax)+
scale_x_reverse(limits=c(400, -200))+
raincloud_theme
print(plt)
} else if (NMRmeth == "MMM") {
raincloud_theme = theme(
text = element_text(size = 16),
axis.title.x=element_text(size = 16),
axis.title.y = element_text(size = 16),
axis.text = element_text(size = 16),
axis.text.x = element_text(angle = 0, vjust = 0.5),
legend.title=element_blank(),
legend.text=element_text(size=16),
legend.position = c(0.8,0.85),
plot.title = element_text(lineheight=.8, face="bold", size = 16),
panel.border = element_blank(),
panel.background = element_blank(),
panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
axis.line.x = element_line(colour = 'black', size=0.5, linetype='solid'),
axis.line.y = element_line(colour = 'black', size=0.5, linetype='solid'))
colors <- c("Alkyl-C" = "#CC79A7", "Methoxyl/N-Alkyl-C"= "#D55E00", "O-Alkyl-C" = "#0072B2", "Di-O-Alkyl-C" = "#F0E442",
"Aromatic-C" = "#56B4E9", "Phenolic-C" = "#E69F00", "Carbonyl and amide-C" = "#999999", "Ketone-C" = "#009E73")
## plot the coordinate system
plt <- ggplot(data = output.spec, mapping = aes(x = ppm, y = norm.intensity)) +
scale_fill_manual(breaks = c("Alkyl-C", "Methoxyl/N-Alkyl-C", "O-Alkyl-C", "Di-O-Alkyl-C", "Aromatic-C",
"Phenolic-C", "Carbonyl and amide-C", "Ketone-C"),
values=colors,
labels = c("Alkyl-C", "Methoxyl/N-Alkyl-C", "O-Alkyl-C", "Di-O-Alkyl-C", "Aromatic-C",
"Phenolic-C", "Carbonyl and amide-C","Ketone-C"))+
## area of Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm >= 0 & ppm <= 45, ppm,NA), y = norm.intensity, fill = "Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of Methoxyl-C
geom_area(mapping = aes(x = ifelse(ppm> 45 & ppm< 60 , ppm, NA), y = norm.intensity, fill = "Methoxyl/N-Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of O-Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm> 60 & ppm< 95 , ppm, NA), y = norm.intensity, fill = "O-Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of Di-O-Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm> 95 & ppm< 110 , ppm, NA), y = norm.intensity, fill = "Di-O-Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of H and C substituted aromatic -C
geom_area(mapping = aes(x = ifelse(ppm> 110 & ppm< 145 , ppm, NA), y = norm.intensity, fill = "Aromatic-C"), alpha = 0.8, size = 0.5) +
## area of O substituted aromatic -C
geom_area(mapping = aes(x = ifelse(ppm> 145 & ppm< 165 , ppm, NA), y = norm.intensity, fill = "Phenolic-C"), alpha = 0.8, size = 0.5) +
## area of carboxyl-C
geom_area(mapping = aes(x = ifelse(ppm> 165 & ppm< 190 , ppm, NA), y = norm.intensity, fill = "Carbonyl and amide-C"), alpha = 0.8, size = 0.5) +
## area of carboxyl-C
geom_area(mapping = aes(x = ifelse(ppm> 190 & ppm< 210 , ppm, NA), y = norm.intensity, fill = "Ketone-C"), alpha = 0.8, size = 0.5) +
## plot the NMR spectrum
geom_line(size = 0.25)+
## Axis title
xlab("Chemical shift (ppm)") +
ylab("Intensity")+
## create line y = 0
ylim(-5, plot.ymax)+
scale_x_reverse(limits=c(400, -200))+
raincloud_theme
print(plt)
}
## close image file
if (file.output == TRUE) {
dev.off()
} else {
print(plt)
}
}
return(plt)
## close function
}
Try the SOMnmR package in your browser
Any scripts or data that you put into this service are public.
SOMnmR documentation built on July 4, 2024, 9:06 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' NMR Plotting Function
#'
#' This function allows you to plot the 13C-NMR spectra using marking different integration regions.
#' The loaded Raw spectra are intensity normalized and plotted with the chosen integration regions, either spinning side bands (default),
#' the Bonanomi("Bonanomi") regions or the Molecular Mixing Model regions("MMM").
#' The function returns the plots as images either tiff or png, normalized and flattened spectrum
#' @param raw.spec loaded NMR spectra
#' @param NMRmeth Regions to be integrated, methods available include: "4region", "Bonanomi", "Smernik" and Molecular mixing model ("MMM").
#' @param use.tiff Logical, default to FALSE (use png)
#' @param set.plot.ymax Set maximum of plot y axis, defaults to NULL
#' @param file.output Logical, default to FALSE
#' @returns A plot of the NMR spectrum and a csv file of the data plotted.
#' @keywords normalization integration
#' @export
#' @import ggplot2
#' @examples
#' \donttest{
#' library(ggplot2)
#' data("GarciaF200")
#' plot_NMR(GarciaF200, NMRmeth = "MMM", file.output = FALSE, use.tiff = FALSE)
#' }
plot_NMR <- function (raw.spec, NMRmeth = NULL, use.tiff = NULL,
set.plot.ymax = NULL, file.output = NULL) {
## check and assign FALSE if optional parameters are not set
if(is.null(use.tiff)) {use.tiff <- FALSE}
if(is.null(file.output)) {file.output <- FALSE}
for (i in 1:length(raw.spec)) {
sample.name <- raw.spec[[i]]$name
corr.spec <- raw.spec[[i]]$data$raw.spec
corr.spec$raw.intensity <- (corr.spec$raw.intensity/max(corr.spec$raw.intensity))*100
## create list of new sample for fitting function
new.spec <- list("name" = raw.spec[[i]]$name, "data" = list("corr.spec" = corr.spec))
ppm <- NULL
norm.intensity <- NULL
if (file.output == TRUE) {
output.spec <- data.frame(cbind(ppm = corr.spec$ppm, norm.intensity = corr.spec$raw.intensity))
write.csv2(output.spec, paste("output.", sample.name, "csv", sep = "."), row.names = FALSE)
} else if (file.output == FALSE) {
output.spec <- data.frame(cbind(ppm = corr.spec$ppm, norm.intensity = corr.spec$raw.intensity))
}
## create image file name with high resolution (png or tiff)
if (file.output == TRUE) {
if (use.tiff == TRUE) {
tiff(filename = paste(sample.name, "normalized.tiff", sep = "."),
width = 3200, height = 3200, units = "px", res = 400,
compression = c("none"))
} else {
png(filename = paste(sample.name, "normalized.png", sep = "."),
width = 3200, height = 3200, units = "px", res = 400)
}
## create header name
head.name <- paste(sample.name, "normalized", sep = " ")
} else {
## simply use sample name as header name
head.name <- paste(sample.name)
}
## preserving old parameters
oldpar <- par(no.readonly = TRUE)
# Ensure the original graphical parameters are restored on exit
on.exit(par(oldpar))
## set squared plots (pty), margins (mar), and size of plot (cex)
if (file.output == TRUE) {
par(pty="s",
mar=c(5,3,2,0)+0.1, # c(bottom, left, top, right)
cex = 0.5
)
}
if (is.null(set.plot.ymax)) {
plot.ymax <- max(output.spec$norm.intensity)+0.5
} else {
plot.ymax <- set.plot.ymax
}
if (is.null(NMRmeth)) {
raincloud_theme = theme(
text = element_text(size = 16),
axis.title.x=element_text(size = 16),
axis.title.y = element_text(size = 16),
axis.text = element_text(size = 16),
axis.text.x = element_text(angle = 0, vjust = 0.5),
legend.title=element_blank(),
legend.text=element_text(size=16),
legend.position = c(0.8,0.85),
plot.title = element_text(lineheight=.8, face="bold", size = 16),
panel.border = element_blank(),
panel.background = element_blank(),
panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
axis.line.x = element_line(colour = 'black', size=0.5, linetype='solid'),
axis.line.y = element_line(colour = 'black', size=0.5, linetype='solid'))
colors <- c("Alkyl-C" = "#CC79A7", "O/N-Alkyl-C" = "#0072B2", "Aryl-C" = "#E69F00", "Carboxyl-C" = "#009E73")
## plot the coordinate system
plt <- ggplot(data = output.spec, mapping = aes(x = ppm, y = norm.intensity)) +
scale_fill_manual(breaks = c("Alkyl-C", "O/N-Alkyl-C", "Aryl-C", "Carboxyl-C"),values=colors, labels = c("Alkyl-C", "O/N-Alkyl-C", "Aryl-C", "Carboxyl-C"))+
## area of Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm>0 & ppm< 45 , ppm, NA), fill = "Alkyl-C"), alpha = 0.8, size = 0.6) +
## area of O Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm>45 & ppm< 110 , ppm, NA), fill = "O/N-Alkyl-C"), alpha = 0.8, size = 0.6) +
## area of Aryl-C
geom_area(mapping = aes(x = ifelse(ppm>110 & ppm< 160 , ppm, NA), fill = "Aryl-C"), alpha = 0.8, size = 0.6) +
## area of carboxyl-C
geom_area(mapping = aes(x = ifelse(ppm>160 & ppm< 220 , ppm, NA), fill = "Carboxyl-C"), alpha = 0.8, size = 0.6) +
## plot the NMR spectrum
geom_line(size = 0.25)+
## Axis title
xlab("Chemical shift (ppm)") +
ylab("Intensity")+
## create line y = 0
ylim(-5, plot.ymax)+
scale_x_reverse(limits=c(400, -200))+
raincloud_theme
print(plt)
} else if (NMRmeth == "Smernik") {
raincloud_theme = theme(
text = element_text(size = 16),
axis.title.x=element_text(size = 16),
axis.title.y = element_text(size = 16),
axis.text = element_text(size = 16),
axis.text.x = element_text(angle = 0, vjust = 0.5),
legend.title=element_blank(),
legend.text=element_text(size=16),
legend.position = c(0.8,0.85),
plot.title = element_text(lineheight=.8, face="bold", size = 16),
panel.border = element_blank(),
panel.background = element_blank(),
panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
axis.line.x = element_line(colour = 'black', size=0.5, linetype='solid'),
axis.line.y = element_line(colour = 'black', size=0.5, linetype='solid'))
colors <- c("Alkyl-C" = "#CC79A7", "O/N-Alkyl-C" = "#0072B2", "Aryl-C" = "#E69F00", "Carboxyl-C" = "#009E73")
## plot the coordinate system
plt <- ggplot(data = output.spec, mapping = aes(x = ppm, y = norm.intensity)) +
scale_fill_manual(breaks = c("Alkyl-C", "O/N-Alkyl-C", "Aryl-C", "Carboxyl-C"),values=colors, labels = c("Alkyl-C", "O/N-Alkyl-C", "Aryl-C", "Carboxyl-C"))+
## area of Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm>0 & ppm< 45 , ppm, NA), fill = "Alkyl-C"), alpha = 0.8, size = 0.6) +
## area of O Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm>45 & ppm< 110 , ppm, NA), fill = "O/N-Alkyl-C"), alpha = 0.8, size = 0.6) +
## area of Aryl-C
geom_area(mapping = aes(x = ifelse(ppm>110 & ppm< 165 , ppm, NA), fill = "Aryl-C"), alpha = 0.8, size = 0.6) +
## area of carboxyl-C
geom_area(mapping = aes(x = ifelse(ppm>165 & ppm< 185 , ppm, NA), fill = "Carboxyl-C"), alpha = 0.8, size = 0.6) +
## plot the NMR spectrum
geom_line(size = 0.25)+
## Axis title
xlab("Chemical shift (ppm)") +
ylab("Intensity")+
## create line y = 0
ylim(-5, plot.ymax)+
scale_x_reverse(limits=c(400, -200))+
raincloud_theme
print(plt)
} else if (NMRmeth == "Bonanomi") {
raincloud_theme = theme(
text = element_text(size = 16),
axis.title.x=element_text(size = 16),
axis.title.y = element_text(size = 16),
axis.text = element_text(size = 16),
axis.text.x = element_text(angle = 0, vjust = 0.5),
legend.title=element_blank(),
legend.text=element_text(size=16),
legend.position = c(0.8,0.85),
plot.title = element_text(lineheight=.8, face="bold", size = 16),
panel.border = element_blank(),
panel.background = element_blank(),
panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
axis.line.x = element_line(colour = 'black', size=0.5, linetype='solid'),
axis.line.y = element_line(colour = 'black', size=0.5, linetype='solid'))
colors <- c("Alkyl-C" = "#CC79A7", "Methoxyl/N-Alkyl-C"= "#D55E00", "O-Alkyl-C" = "#0072B2", "Di-O-Alkyl-C" = "#F0E442",
"Aromatic-C" = "#56B4E9", "Phenolic-C" = "#E69F00", "Carbonyl and amide-C" = "#999999", "Ketone-C" = "#009E73")
## plot the coordinate system
plt <- ggplot(data = output.spec, mapping = aes(x = ppm, y = norm.intensity)) +
scale_fill_manual(breaks = c("Alkyl-C", "Methoxyl/N-Alkyl-C", "O-Alkyl-C", "Di-O-Alkyl-C", "Aromatic-C",
"Phenolic-C", "Carbonyl and amide-C", "Ketone-C"),
values=colors,
labels = c("Alkyl-C", "Methoxyl/N-Alkyl-C", "O-Alkyl-C", "Di-O-Alkyl-C", "Aromatic-C",
"Phenolic-C", "Carbonyl and amide-C","Ketone-C"))+
## area of Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm >= 0 & ppm <= 45, ppm,NA), y = norm.intensity, fill = "Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of Methoxyl-C
geom_area(mapping = aes(x = ifelse(ppm> 46 & ppm< 60 , ppm, NA), y = norm.intensity, fill = "Methoxyl/N-Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of O-Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm> 61 & ppm< 90 , ppm, NA), y = norm.intensity, fill = "O-Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of Di-O-Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm> 91 & ppm< 110 , ppm, NA), y = norm.intensity, fill = "Di-O-Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of H and C substituted aromatic -C
geom_area(mapping = aes(x = ifelse(ppm> 111 & ppm< 140 , ppm, NA), y = norm.intensity, fill = "Aromatic-C"), alpha = 0.8, size = 0.5) +
## area of O substituted aromatic -C
geom_area(mapping = aes(x = ifelse(ppm> 141 & ppm< 160 , ppm, NA), y = norm.intensity, fill = "Phenolic-C"), alpha = 0.8, size = 0.5) +
## area of carboxyl-C
geom_area(mapping = aes(x = ifelse(ppm> 161 & ppm< 190 , ppm, NA), y = norm.intensity, fill = "Carbonyl and amide-C"), alpha = 0.8, size = 0.5) +
## plot the NMR spectrum
geom_line(size = 0.25)+
## Axis title
xlab("Chemical shift (ppm)") +
ylab("Intensity")+
## create line y = 0
ylim(-5, plot.ymax)+
scale_x_reverse(limits=c(400, -200))+
raincloud_theme
print(plt)
} else if (NMRmeth == "MMM") {
raincloud_theme = theme(
text = element_text(size = 16),
axis.title.x=element_text(size = 16),
axis.title.y = element_text(size = 16),
axis.text = element_text(size = 16),
axis.text.x = element_text(angle = 0, vjust = 0.5),
legend.title=element_blank(),
legend.text=element_text(size=16),
legend.position = c(0.8,0.85),
plot.title = element_text(lineheight=.8, face="bold", size = 16),
panel.border = element_blank(),
panel.background = element_blank(),
panel.grid.minor = element_blank(),
panel.grid.major = element_blank(),
axis.line.x = element_line(colour = 'black', size=0.5, linetype='solid'),
axis.line.y = element_line(colour = 'black', size=0.5, linetype='solid'))
colors <- c("Alkyl-C" = "#CC79A7", "Methoxyl/N-Alkyl-C"= "#D55E00", "O-Alkyl-C" = "#0072B2", "Di-O-Alkyl-C" = "#F0E442",
"Aromatic-C" = "#56B4E9", "Phenolic-C" = "#E69F00", "Carbonyl and amide-C" = "#999999", "Ketone-C" = "#009E73")
## plot the coordinate system
plt <- ggplot(data = output.spec, mapping = aes(x = ppm, y = norm.intensity)) +
scale_fill_manual(breaks = c("Alkyl-C", "Methoxyl/N-Alkyl-C", "O-Alkyl-C", "Di-O-Alkyl-C", "Aromatic-C",
"Phenolic-C", "Carbonyl and amide-C", "Ketone-C"),
values=colors,
labels = c("Alkyl-C", "Methoxyl/N-Alkyl-C", "O-Alkyl-C", "Di-O-Alkyl-C", "Aromatic-C",
"Phenolic-C", "Carbonyl and amide-C","Ketone-C"))+
## area of Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm >= 0 & ppm <= 45, ppm,NA), y = norm.intensity, fill = "Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of Methoxyl-C
geom_area(mapping = aes(x = ifelse(ppm> 45 & ppm< 60 , ppm, NA), y = norm.intensity, fill = "Methoxyl/N-Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of O-Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm> 60 & ppm< 95 , ppm, NA), y = norm.intensity, fill = "O-Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of Di-O-Alkyl-C
geom_area(mapping = aes(x = ifelse(ppm> 95 & ppm< 110 , ppm, NA), y = norm.intensity, fill = "Di-O-Alkyl-C"), alpha = 0.8, size = 0.5) +
## area of H and C substituted aromatic -C
geom_area(mapping = aes(x = ifelse(ppm> 110 & ppm< 145 , ppm, NA), y = norm.intensity, fill = "Aromatic-C"), alpha = 0.8, size = 0.5) +
## area of O substituted aromatic -C
geom_area(mapping = aes(x = ifelse(ppm> 145 & ppm< 165 , ppm, NA), y = norm.intensity, fill = "Phenolic-C"), alpha = 0.8, size = 0.5) +
## area of carboxyl-C
geom_area(mapping = aes(x = ifelse(ppm> 165 & ppm< 190 , ppm, NA), y = norm.intensity, fill = "Carbonyl and amide-C"), alpha = 0.8, size = 0.5) +
## area of carboxyl-C
geom_area(mapping = aes(x = ifelse(ppm> 190 & ppm< 210 , ppm, NA), y = norm.intensity, fill = "Ketone-C"), alpha = 0.8, size = 0.5) +
## plot the NMR spectrum
geom_line(size = 0.25)+
## Axis title
xlab("Chemical shift (ppm)") +
ylab("Intensity")+
## create line y = 0
ylim(-5, plot.ymax)+
scale_x_reverse(limits=c(400, -200))+
raincloud_theme
print(plt)
}
## close image file
if (file.output == TRUE) {
dev.off()
} else {
print(plt)
}
}
return(plt)
## close function
}
Try the SOMnmR package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.