ProteinMS_Spectra_FinalProject

Read files into data frames:

standardSpectra = read.table("07-18-2025_f3_0001_F3_25-07-18_15-52_0001.txt", header = FALSE, skip = 8)
sampleSpectra = read.table("07-18-2025_f4_0001_F4_25-07-18_15-53_0001.txt", header = FALSE, skip = 8)

##Remove first outlier + give column names:

standardSpectra = standardSpectra[-1,]
sampleSpectra = sampleSpectra[-1,]
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')

##Graph P!

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

ggplot(ms_data, aes(x = mz,y=intensity))+
  geom_col(aes(colour = type ,fill=type))+
  scale_color_manual(values=c("#FFC0CB","#c5f19d"))+
  scale_fill_manual(values=c("#FFC0CB","#c5f19d"))+
  xlab("m/z ratio") + ylab("Millivolts")+
  xlim(0,1000)+
  theme(legend.position="right")

## Warning: Removed 2 rows containing missing values or values outside the scale range
## (`geom_col()`).

##Graph G / Facet Wrap:

ggplot(ms_data, aes(x = mz,y=intensity))+
  geom_col(aes(colour = type ,fill=type))+
  scale_color_manual(values=c("#FFC0CB","#c5f19d"))+
  scale_fill_manual(values=c("#FFC0CB","#c5f19d"))+
  xlab("m/z ratio") + ylab("Millivolts")+
  xlim(0,1000)+
  facet_wrap(~type,nrow=2)

## Warning: Removed 2 rows containing missing values or values outside the scale range
## (`geom_col()`).