Plot_MS_Spectra

#Reading in files from Shimadzu MALDI-TOF into dataframes

standardSpectra <- read.table('C3_0001_C3_25-07-18_15-59_0001.txt', header = FALSE, skip = 8)
sampleSpectra <- read.table('C4_0001_C4_25-07-18_16-00_0001.txt', header = FALSE, skip = 8)

#Removing outlier from first row of dataset

#standardSpectra <- standardSpectra [-1,]
#sampleSpectra <- sampleSpectra [-1,]
#names(standardSpectra) <- c('m_z', 'intensity')
#names(sampleSpectra) <- c('m_z', 'intensity')

#Tidy data (installing Tidyverse)

#installing tidyverse
library(tidyverse)

## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr     1.1.4     ✔ readr     2.1.5
## ✔ forcats   1.0.0     ✔ stringr   1.5.1
## ✔ ggplot2   3.5.2     ✔ tibble    3.3.0
## ✔ lubridate 1.9.4     ✔ tidyr     1.3.1
## ✔ purrr     1.1.0     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

#Combining sampleSpectra & standardSpectra into one dataset (ms_data)
sampleSpectra$type <- 'Sample'
standardSpectra$type <- 'Standard'
ms_data <- rbind(sampleSpectra,standardSpectra)
names(ms_data) <-c('mz', 'intensity', 'type')

#Creating a ggplot from the data

#Column overlap plot
ggplot(ms_data, aes(x = mz,y=intensity))+
  geom_col(aes(colour = type,fill=type))+
  scale_color_manual(values=c("#ffc868","#e5216b"))+
  scale_fill_manual(values=c("#ffc868","#e5216b"))+
  xlab("m/z Ratio") + ylab("Millivolts")+
  theme(legend.position="right")

#Separate column plots
ggplot(ms_data, aes(x = mz,y=intensity))+
  geom_col(aes(colour = type,fill=type))+
  scale_color_manual(values=c("#ffc868","#e5216b"))+
  scale_fill_manual(values=c("#ffc868","#e5216b"))+
  xlab("m/z Ratio") + ylab("Millivolts")+
  facet_wrap(~type,nrow=2)

#Matching Spectra

matchSpectra <- merge(standardSpectra, sampleSpectra, by="V1")
write.csv(matchSpectra,"matchSpectra.csv")