R/plot_display.R

In yuriychen/MSPlotcyl: MS spectrum plot

#' @title Read MS data in mzXML format.
#' @description Read MS data in mzXML format.
#' @details Input a file path of mzXML format, then return a data set. The mzXML format file can be transformed wi MSConvert software.
#' @param filepath A string of mzXML file location.
#' @return A list.
#' @export
#' @import readMzXmlData
data_read_mzXML <- function(filepath){
  #readMzXmlFile from readMzXmlData lib
  mzXML <- readMzXmlFile(filepath)

  return(mzXML)
}

#' @title Plot MS2 spectrum with b, y ions.
#' @description Plot MS2 spectrum with b, y ions.
#' @details Input a mzXML from data_read_mzXML function and scan number and peptide sequence, then return a list of ggplot objects.
#' @param mzXML A data set from data_read_mzXML function.
#' @param scan_num A integer.
#' @param pep_seq A string of peptide sequence.
#' @param threshold A integer of mz error with defalut .5.
#' @return A list of ggplot2 object.
#' @export
#' @import ggplot2
#' @import ggrepel
#' @import dplyr
data_ms2_by_plot <- function(mzXML, scan_num, pep_seq = '', threshold = .5){
  df_mass_inten <- data.frame(mzXML[[scan_num]][1])
  colnames(df_mass_inten) <- c('mass','intensity')

  if(pep_seq == ''){
    #ggplot from ggplot2 lib
    #ggrepel from ggrepel lib
    p <- ggplot(df_mass_inten, aes(x=mass,y=intensity))+geom_segment(aes(xend=mass,yend=0),size=1.25)
    p <- p + xlab('m/z') + ylab('Intensity') + theme_bw() + theme(axis.title = element_text(size=15),legend.position = 'none')

    return(p)
  }

  if(pep_seq != ''){
    df_ions <- calculate_byions(pep_seq=pep_seq, cal_ion_list=cal_ion_list)

    for (t in rownames(df_ions)){
      temp <- df_mass_inten
      temp$deltamass <- abs(temp$mass - df_ions[t,'mz'])
      temp <- temp[order(temp$deltamass),]

      if (temp$deltamass[1] < threshold){
        df_mass_inten$ion[(df_mass_inten$mass == (temp$mass[1]))] <- df_ions[t,'ion']
        df_mass_inten$iontype[(df_mass_inten$mass == (temp$mass[1]))] <- strsplit(df_ions[t,'ion'],split = '')[[1]][1]
      }
    }
    #left_join from dplyr lib
    ion_list <- left_join(df_ions,df_mass_inten)
    ion_list$iontype[is.na(ion_list$iontype)] <- '-'
    print(ion_list)
    ion_list_clean <- ion_list[!is.na(ion_list$mass),]
    #ggplot from ggplot2 lib
    #ggrepel from ggrepel lib
    p <- ggplot(df_mass_inten, aes(x=mass,y=intensity, color=iontype))+geom_segment(aes(xend=mass,yend=0),size=1.25, alpha=.5)+
      geom_text_repel(subset(df_mass_inten,(iontype=='b' | iontype=='y')),mapping=aes(label=ion_list_clean[order(ion_list_clean[,3]),2]),size=7,hjust=-.5, vjust= -.5, max.iter = 1e4)
    p <- p + xlab('m/z') + ylab('Intensity') + theme_bw() + theme(axis.title = element_text(size=15),legend.position = 'none')

    pseq <- data_fragment_plot(pep_seq = pep_seq, ion_list = ion_list)

    return(list(p,pseq))
  }
}

data_fragment_plot <- function(pep_seq, ion_list){
  x <- data.frame(cbind(seq(1,nchar(pep_seq)),rep(1,nchar(pep_seq))))
  colnames(x) <- c('x','y')
  p <- ggplot(x,aes(x=x,y=y))+geom_text(aes(label= (strsplit(pep_seq,split = '')[[1]])),size=20,vjust=.5,hjust=.5)+ylim(0,2)

  ion_1 <- ion_list[1:(nrow(ion_list) / 2),]
  icount <- 1
  for (i in ion_1[,'iontype']) {
    if (i != '-') {
      p <- p + geom_segment(x=(icount - .25),xend=(icount + .55),y=1.2,yend=1.2,size=2,color='indianred1') + geom_segment(x=(icount + .5),xend=(icount + .5),y=1,yend=1.2,size=2,color='indianred1')
    }
    icount <- icount + 1
  }

  ion_2 <- ion_list[(nrow(ion_list) / 2 + 1) : nrow(ion_list),]
  icount <- nrow(ion_2)
  for (i in ion_2[,'iontype']) {
    if (i != '-') {
      p <- p + geom_segment(x=(icount - .525),xend=(icount + .25),y=.8,yend=.8,size=2,color='#7CE3D8') + geom_segment(x=(icount - .5),xend=(icount - .5),y=.8,yend=1,size=2,color='#7CE3D8')
    }
    icount <- icount - 1
  }

  p <- p + theme(axis.title = element_blank(), axis.text = element_blank(), axis.line = element_blank(),axis.ticks = element_blank(),panel.grid = element_blank(),panel.border = element_blank(),panel.background = element_blank())

  return(p)
}