#Display EDX spectrum from psma file
##Import the different spectra files

read.table(sep = ",", file = "/path/to/file.psmsa") -> EDX_data


#assigning first column to keV and second column to counts

EDX_data[,1] -> KeV
EDX_data[,2]-> counts

# Libraries
library(ggplot2)

# create data

data <- data.frame(KeV,counts)

# Plot function
plot_spectrum <- function(data) {
 # data[,1] -> KeV
 # data[,2]-> counts
  ggplot(data, aes(x = KeV, y = counts)) + 
    geom_area(fill = "#0190a2", alpha = 0.4) + #color to fill under the line
    geom_line(color = "blue", size = 0.5) + #color and thickness of the line
    scale_x_continuous(n.breaks = 10, limits = c(0, 20)) + #number of x-axis values diplayed, limit values of the x axis
    theme(axis.text.x = element_text(angle = 90)) + #rotate x-axis labels 90°
    geom_vline(xintercept = c(0.5, 1.09, 1.74, 2.12, 2.042, 2.048), linetype = "dotted", size = 0.5) + #diplay vertical dotted lines where the expected peaks are 
    ggtitle(paste("Spectrum Plot -", deparse(substitute(data)))) +  # Dynamic title based on data name
    xlab("KeV") +              # Add x-axis label
    ylab("Counts")             # Add y-axis label
}

#Create plot

plot_spectrum(EDX_data)