Script to read in and plot MS Spectra from Shimadzu MALDI-TOF

Step 1: Read files into dataframes

standardSpectra <- read.table('G3_0001_G3_25-07-18_15-50_0002.txt',header=FALSE,skip=8)
sampleSpectra <- read.table('G4_0001_G4_25-07-18_15-51_0001.txt',header=FALSE,skip=8)

#Remove outlier in first row and add column names

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

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

#simple plot with lines for spectra

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")

#facet wrap

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)