BIN521L-Lab

Script to read in plot MS Spectra from Shimadzu Madldi-TDF

Step 1: Read files into dataframes

standardSpectra <- read.table('D3_0001_D3_25-07-18_15-57_0001.txt',header=FALSE,skip=8)
sampleSpectra <- read.table('D4_0001_D4_25-07-18_15-58_0001.txt',header=FALSE,skip=8)

#Remove outlier in next Row

#standardSpectra <-standardSpectra {-1,}
#sampleSpectra <-sampleSpectra {-1,}
#names(standardSpectra) <- c('m_2','intesnsity')
#names(sampleSpectra) <- c (('m_2','intesnsity')

tidy data

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

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

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")

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

#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)