Plot MS Spectra

Script to read in an plot MS Spectra from Shimadzu MALDI-TOf

#Read files into dataframes

standardSpectra <- read.table('B3_0001_B3_25-07-18_16-01_0001.txt',header=FALSE, skip=8)
sampleSpectra <- read.table('B4_0001_B4_25-07-18_16-02_0001.txt',header=FALSE, skip=8)

#Remove outlier in first row

standardSpectra <- standardSpectra[-1,]
standardSpectra <- standardSpectra[standardSpectra$V1<3000,]
sampleSpectra <- sampleSpectra[-1,]
sampleSpectra <- sampleSpectra[sampleSpectra$V1<3000,]
names(standardSpectra) <- c('m_z', 'intensity')
names(sampleSpectra) <- c('m_z', 'intensity')

#Tidy data

library(tidyverse)

## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
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## ✔ 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

sampleSpectra$type <- 'Sample'
standardSpectra$type <- 'Standard'
ms_data <- rbind(sampleSpectra,standardSpectra)
names(ms_data)<-c('mz','intensity','type')

#Column plot

p <- ggplot(ms_data, aes(x = mz,y=intensity))+
  geom_col(aes(colour = typep
               ,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")

#facet wrap

p2 <- 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)