R/plot_components.R
In lileir/mms2plot: Visualization of multiple MS/MS spectra for modified and non-modified peptides
Defines functions
generate_ionLabel
label_axis
# label x/y axis
label_axis<-function(max_intensity, xlab, ylab, max_mz, cex,lwd){
if(length(max_intensity) == 2){ # for mirror_plot
if( max_intensity[1] > 0){ # quarter of the max_intensity
axis_y_positive <- seq(0, max_intensity[1], length.out = 5)
axis_y_negative <- seq(max_intensity[2], 0, length.out = 5)
}else{# quarter of the max_intensity
axis_y_positive <- seq(max_intensity[1], 0, length.out = 5)
axis_y_negative <- seq(0, max_intensity[2], length.out = 5)
}
# remove duplicate "0" and keep 4 digits
axis_y <- signif(c(axis_y_negative, axis_y_positive[-1]), digits=4)
# abs( separate -1 to 1 with the length of 9 )
axis_y_percent <- scales::percent(abs(seq(-1, 1, length.out = 9)))
axis(side = 2,las = 1, at = seq(-1,1, length.out = 9),
labels = as.integer(axis_y), tck=-0.01, mgp=c(0, 0.2, 0),
cex.axis=0.33, lwd=0.5*lwd)
axis(side = 4,las = 1, at = seq(-1,1, length.out = 9),
labels = axis_y_percent, tck=-0.01, mgp=c(0, 0.2, 0),
cex.axis=0.33, lwd=0.5*lwd)
axis(side = 1, at=seq(0, max_mz, by=200), lwd=0.5*lwd, tck=-0.01,
labels=FALSE)
# mgp=c(0,0.1,0) NOT work for dist. betw. label and x-axis. mtext used.
graphics::mtext(side = 1, text=seq(0, max_mz, by=200),
at=seq(0, max_mz, by=200), cex=0.33*cex) #
}else{ # for group_plot
axis_y <- seq(0, max_intensity, length.out = 5)
axis_y_percent <- scales::percent(seq(0, 1, length.out = 5))
axis(side = 2,las = 1, at = seq(0, 1, length.out = 5),
labels = as.integer(axis_y), tck=-0.02, mgp=c(0, 0.2, 0),
cex.axis=0.33, lwd=0.5*lwd)
axis(side = 4,las = 1, at = seq(0, 1, length.out = 5),
labels = axis_y_percent, tck=-0.02, mgp=c(0, 0.2, 0),
cex.axis=0.33, lwd=0.5*lwd)
}
}
generate_ionLabel <- function(ionLabel_peak, show_iontype){
#browser()
# ionLabel_peaks_split = unlist(strsplit(ionLabel_peak), ",")
# for(i in 1:length(ionLabel_peaks_split)){
# ionLabel_peak = ionLabel_peaks_split[i]
# ion_name <- substr(ionLabel_peak, 1, regexpr(pattern ='\\+', ionLabel_peak)-1)
# number_plus <- substring(ionLabel_peak, regexpr(pattern ='\\+',ionLabel_peak))
# if(number_plus == "+"){number_plus = ""}
# else if(number_plus == "+*"){number_plus="*"}
# else if(number_plus == "++"){number_plus="2+"}
# else if(number_plus == "++*"){number_plus="2+*"}
#
# if(grepl("^z0", ion_name )){
# ion_number = substring(ion_name, 3)
# if(show_iontype){
# label = as.expression(bquote('z'^o*.(ion_number)^.(number_plus)))
# }else{
# label = as.expression(bquote(.(ion_number)^.(number_plus)))
# }
# }else{
# if(show_iontype){
# label = as.expression(bquote(.(ion_name)^.(number_plus)))
# }else{
# ion_name = substring(ion_name, 2)
# label = as.expression(bquote(.(ion_name)^.(number_plus)))
# }
# }
# }
show_iontype=T
# ionLabel_peak = "z08++,y7+"
# ionLabel_peak = "z08++"
ionLabel_peak = gsub("z0", "w", ionLabel_peak)
if(grepl(",", ionLabel_peak)){
ionLabel_peak = unlist(strsplit(ionLabel_peak, ","))
}
ionLabel <- substr(ionLabel_peak, 1, 1)
ionLabel_style <- ifelse(ionLabel == "w", "o", "")
ionLabel = gsub("w", "z", ionLabel)
ionLabel_number <- substr(ionLabel_peak, 2, regexpr(pattern ='\\+', ionLabel_peak)-1)
number_plus <- substring(ionLabel_peak, regexpr(pattern ='\\+',ionLabel_peak))
number_plus = gsub("^\\+\\+", "2+", number_plus)
number_plus = gsub("^\\+", "", number_plus)
if(length(ionLabel) == 1){
label = as.expression(bquote(.(ionLabel)^.(ionLabel_style)*.(ionLabel_number)^.(number_plus)))
}else if(length(ionLabel) == 2){
label = as.expression(bquote(paste(.(ionLabel[1])^.(ionLabel_style[1])*.(ionLabel_number[1])^.(number_plus[2]),",",.(ionLabel[2])^.(ionLabel_style[2])*.(ionLabel_number[2])^.(number_plus[2]),sep="")))
# label = as.expression(bquote(.(ionLabel[1])^.(ionLabel_style[1])*.(ionLabel_number[1])^.(number_plus[2]),.(ionLabel[2])^.(ionLabel_style[2])*.(ionLabel_number[2])^.(number_plus[2])))
}
# if(length(ionLabel_peak) == 1){
# if(grepl("^z0", ion_name )){
# ion_number = substring(ion_name, 3)
# if(show_iontype){
# label = as.expression(bquote('z'^o*.(ion_number)^.(number_plus)))
# }else{
# label = as.expression(bquote(.(ion_number)^.(number_plus)))
# }
# }else{
# if(show_iontype){
# label = as.expression(bquote(.(ion_name)^.(number_plus)))
# }else{
# ion_name = substring(ion_name, 2)
# label = as.expression(bquote(.(ion_name)^.(number_plus)))
# }
# }
# }
return(label)
}
# peaks annotation plot(rnorm(30), xlab = as.expression(bquote(.(a)^th*.(b))))
####################
draw_peak_ionL<-function(psm, lwd, len_annoSpace, srt,show_iontype){
#browser()
len_annoSpace = 0.05 # len_annoSpace / 2 distance between peak and label
ion_unique<-unique(psm, select=c("mz", "abs_intensity_prc_ext", "direction",
"intensity_perc","ionLabel_peak","col"))
lines(ion_unique$mz, ion_unique$intensity_perc, type = "h",las=1,
col=ion_unique$col, lwd = lwd/2)
segments(ion_unique$mz,ion_unique$intensity_perc, ion_unique$mz,
ion_unique$abs_intensity_prc_ext*ion_unique$direction,
col=ion_unique$col, lwd = lwd/2, lty=3) # draw peak extention segments
labels = mapply(generate_ionLabel, ion_unique$ionLabel_peak, show_iontype)
text( ion_unique$mz, (ion_unique$abs_intensity_prc_ext+len_annoSpace)
*ion_unique$direction,
labels <- labels, cex = 0.3, col=ion_unique$col,adj=0.5,srt=0)
#browser()
}
# generate and draw PSM labels
draw_psmanno<-function(AA_mz, PSM, max_mz, peptide_height, mod_height,
len_annoSpace, y_ion_col, b_ion_col, lwd){
#browser()
AA_mz = AA_mz[[1]] # change a list of data.frame to data.frame
# for peptide annotation, only consider aa with charge 1 for printing
AA_mz <- subset(AA_mz, AA_mz$charge == 1)
direction <- PSM$direction[1] # draw MS2 on upplot (1) or downplot (-1)
peptide <- c("-", as.character(AA_mz$aa_varmod), "-")
peptide_list <- vector("list", length(peptide)*2-1) # set peptide + two dash
peptide_list_b <- peptide_list # preset NULL for b ions
peptide_list_y <- peptide_list # preset NULL for y ions
peptide_list_c <- peptide_list # preset NULL for c ions
peptide_list_z0 <- peptide_list # preset NULL for z0 ions
peptide_list_z1 <- peptide_list # preset NULL for z1 ions
# set peptide
peptide_list[c(TRUE,FALSE)] <- as.list(peptide)
peptide_list[c(FALSE,TRUE)] <- as.list(".")
# set b ions
peptide_list_b[c(FALSE,TRUE)] <-
paste("b", seq(0,length(peptide)-2,by=1),sep="")
# set y ions
peptide_list_y[c(FALSE,TRUE)] <-
paste("y", rev(seq(0,length(peptide)-2,by=1)), sep="")
# set c ions
peptide_list_c[c(FALSE,TRUE)] <-
paste("c", seq(0,length(peptide)-2,by=1),sep="")
# set z ions
peptide_list_z0[c(FALSE,TRUE)] <-
paste("z0", rev(seq(0,length(peptide)-2,by=1)), sep="")
peptide_list_z1[c(FALSE,TRUE)] <-
paste("z'", rev(seq(0,length(peptide)-2,by=1)), sep="")
# set the width of AA sequence in the plot
x_quarter<-seq(0,max_mz, length.out = 20)[c(3,18)] # seq from 5/20 to 17/20
AA_pos <- seq(x_quarter[1], x_quarter[2], length.out=length(peptide_list))
pos_start_dash <- x_quarter[1] # x-axis value "-" at the front of peptides
pos_end_dash <- x_quarter[2] # x-axis value "-" at the end of peptides
# integrate as data.table
PSMlabel<-data.table::data.table(AA_pos=AA_pos, peptide=peptide_list,
bion=peptide_list_b, yion=peptide_list_y, cion = peptide_list_c,
z0ion = peptide_list_z0, z1ion = peptide_list_z1)
#browser()
apply(PSMlabel, 1, print_modpeptide, peptide_height, mod_height,
pos_start_dash, pos_end_dash, direction)# print AA letters for labelling
# draw b ions between AA letters
PSManno_bion <- subset(PSMlabel, PSMlabel$bion %in% PSM$ion)$AA_pos
index <- match(PSManno_bion,PSMlabel$AA_pos)-1
bion_xsmall <- (PSMlabel$AA_pos[index] + PSManno_bion)/2
PSManno_bsmall <-
substring(subset(PSMlabel, PSMlabel$bion %in% PSM$ion)$bion,2)
# draw y ions between AA letters
PSManno_yion <- subset(PSMlabel, PSMlabel$yion %in% PSM$ion)$AA_pos
index <- match(PSManno_yion,PSMlabel$AA_pos)+1
yion_xlarge <- (PSMlabel$AA_pos[index] + PSManno_yion)/2
PSManno_ysmall <-
substring(subset(PSMlabel, PSMlabel$yion %in% PSM$ion)$yion,2)
# draw c ions between AA letters
PSManno_cion <- subset(PSMlabel, PSMlabel$cion %in% PSM$ion)$AA_pos
index <- match(PSManno_cion,PSMlabel$AA_pos)-1
cion_xsmall <- (PSMlabel$AA_pos[index] + PSManno_cion)/2
PSManno_csmall <-
substring(subset(PSMlabel, PSMlabel$cion %in% PSM$ion)$cion,2)
# draw z0 ions between AA letters
PSManno_z0ion <- subset(PSMlabel, PSMlabel$z0ion %in% PSM$ion)$AA_pos
index <- match(PSManno_z0ion,PSMlabel$AA_pos)+1
z0ion_xlarge <- (PSMlabel$AA_pos[index] + PSManno_z0ion)/2
PSManno_z0small <-
substring(subset(PSMlabel, PSMlabel$z0ion %in% PSM$ion)$z0ion,3) # removing z'
# draw z1 ions between AA letters
PSManno_z1ion <- subset(PSMlabel, PSMlabel$z1ion %in% PSM$ion)$AA_pos
index <- match(PSManno_z1ion,PSMlabel$AA_pos)+1
z1ion_xlarge <- (PSMlabel$AA_pos[index] + PSManno_z1ion)/2
PSManno_z1small <-
substring(subset(PSMlabel, PSMlabel$z1ion %in% PSM$ion)$z1ion,3) # removing z'
#browser()
if(direction ==1){
if(length(PSManno_bion)>0){ # bion
segments(PSManno_bion, rep(peptide_height, length(PSManno_bion)),
PSManno_bion,rep(peptide_height-len_annoSpace,length(PSManno_bion)),
col=b_ion_col, lwd=lwd)
segments(bion_xsmall, rep(peptide_height-len_annoSpace,
length(PSManno_bion)), PSManno_bion,
rep(peptide_height-len_annoSpace, length(PSManno_bion)),
col=b_ion_col, lwd=lwd)
text((bion_xsmall+PSManno_bion)/2, rep(peptide_height-len_annoSpace,
length(PSManno_bion)), PSManno_bsmall, cex = 0.25, adj=c(0.5, 1.3),
col=b_ion_col)
}
if(length(PSManno_yion) > 0 ) { # y ion
segments(PSManno_yion, rep(peptide_height, length(PSManno_yion)),
PSManno_yion,rep(peptide_height+len_annoSpace,length(PSManno_yion)),
col=y_ion_col, lwd=lwd)
segments(yion_xlarge,
rep(peptide_height+len_annoSpace, length(PSManno_yion)),
PSManno_yion, rep(peptide_height+len_annoSpace,
length(PSManno_yion)), col=y_ion_col, lwd=lwd)
text((yion_xlarge+PSManno_yion)/2,
rep(peptide_height+len_annoSpace, length(PSManno_yion)),
PSManno_ysmall, cex = 0.25, adj=c(0.5, -0.3),col=y_ion_col)
}
if(length(PSManno_cion)>0){ # c ion
segments(PSManno_cion, rep(peptide_height, length(PSManno_cion)),
PSManno_cion,rep(peptide_height-len_annoSpace,length(PSManno_cion)),
col=b_ion_col, lwd=lwd)
segments(cion_xsmall, rep(peptide_height-len_annoSpace,
length(PSManno_cion)), PSManno_cion,
rep(peptide_height-len_annoSpace, length(PSManno_cion)),
col=b_ion_col, lwd=lwd)
text((cion_xsmall+PSManno_cion)/2, rep(peptide_height-len_annoSpace,
length(PSManno_cion)), PSManno_csmall, cex = 0.25, adj=c(0.5, 1.3),
col=b_ion_col)
}
if(length(PSManno_z0ion) > 0 ) { #z0 ion
segments(PSManno_z0ion, rep(peptide_height, length(PSManno_z0ion)),
PSManno_z0ion,rep(peptide_height+len_annoSpace,length(PSManno_z0ion)),
col=y_ion_col, lwd=lwd)
segments(z0ion_xlarge,
rep(peptide_height+len_annoSpace, length(PSManno_z0ion)),
PSManno_z0ion, rep(peptide_height+len_annoSpace,
length(PSManno_z0ion)), col=y_ion_col, lwd=lwd)
text((z0ion_xlarge+PSManno_z0ion)/2,
rep(peptide_height+len_annoSpace, length(PSManno_z0ion)),
PSManno_z0small, cex = 0.25, adj=c(0.5, -0.3),col=y_ion_col)
}
if(length(PSManno_z1ion) > 0 ) { # z1 ion
segments(PSManno_z1ion, rep(peptide_height, length(PSManno_z1ion)),
PSManno_z1ion,rep(peptide_height+len_annoSpace,length(PSManno_z1ion)),
col=y_ion_col, lwd=lwd)
segments(z1ion_xlarge,
rep(peptide_height+len_annoSpace, length(PSManno_z1ion)),
PSManno_z1ion, rep(peptide_height+len_annoSpace,
length(PSManno_z1ion)), col=y_ion_col, lwd=lwd)
text((z1ion_xlarge+PSManno_z1ion)/2,
rep(peptide_height+len_annoSpace, length(PSManno_z1ion)),
PSManno_z1small, cex = 0.25, adj=c(0.5, -0.3),col=y_ion_col)
}
}else{
if(length(PSManno_bion)>0){
segments(PSManno_bion, rep(peptide_height*-1, length(PSManno_bion)),
PSManno_bion,
rep((peptide_height+len_annoSpace)*-1, length(PSManno_bion)),
col=b_ion_col, lwd=lwd)
segments(bion_xsmall,
rep((peptide_height+len_annoSpace)*-1, length(PSManno_bion)),
PSManno_bion, rep((peptide_height+len_annoSpace)*-1,
length(PSManno_bion)), col=b_ion_col, lwd=lwd)
text((bion_xsmall+PSManno_bion)/2,rep((peptide_height+len_annoSpace)*-1,
length(PSManno_bion)), PSManno_bsmall, cex = 0.25, adj=c(0.5, 1.3),
col=b_ion_col)
}
if(length(PSManno_yion) > 0 ) {
segments(PSManno_yion, rep(peptide_height*-1, length(PSManno_yion)),
PSManno_yion, rep((peptide_height-len_annoSpace)*-1,
length(PSManno_yion)), col=y_ion_col, lwd=lwd)
segments(yion_xlarge, rep((peptide_height-len_annoSpace)*-1,
length(PSManno_yion)), PSManno_yion,
rep((peptide_height-len_annoSpace)*-1, length(PSManno_yion)),
col=y_ion_col, lwd=lwd)
text((yion_xlarge+PSManno_yion)/2,rep((peptide_height-len_annoSpace)*-1,
length(PSManno_yion)), PSManno_ysmall, cex = 0.25, adj=c(0.5, -0.3),
col=y_ion_col)
}
if(length(PSManno_cion)>0){
segments(PSManno_cion, rep(peptide_height*-1, length(PSManno_cion)),
PSManno_cion,
rep((peptide_height+len_annoSpace)*-1, length(PSManno_cion)),
col=b_ion_col, lwd=lwd)
segments(cion_xsmall,
rep((peptide_height+len_annoSpace)*-1, length(PSManno_cion)),
PSManno_cion, rep((peptide_height+len_annoSpace)*-1,
length(PSManno_cion)), col=b_ion_col, lwd=lwd)
text((cion_xsmall+PSManno_cion)/2,rep((peptide_height+len_annoSpace)*-1,
length(PSManno_cion)), PSManno_csmall, cex = 0.25, adj=c(0.5, 1.3),
col=b_ion_col)
}
if(length(PSManno_z0ion) > 0 ) {
segments(PSManno_z0ion, rep(peptide_height*-1, length(PSManno_z0ion)),
PSManno_z0ion, rep((peptide_height-len_annoSpace)*-1,
length(PSManno_z0ion)), col=y_ion_col, lwd=lwd)
segments(z0ion_xlarge, rep((peptide_height-len_annoSpace)*-1,
length(PSManno_z0ion)), PSManno_z0ion,
rep((peptide_height-len_annoSpace)*-1, length(PSManno_z0ion)),
col=y_ion_col, lwd=lwd)
text((z0ion_xlarge+PSManno_z0ion)/2,rep((peptide_height-len_annoSpace)*-1,
length(PSManno_z0ion)), PSManno_z0small, cex = 0.25, adj=c(0.5, -0.3),
col=y_ion_col)
}
if(length(PSManno_z1ion) > 0 ) {
segments(PSManno_z1ion, rep(peptide_height*-1, length(PSManno_z1ion)),
PSManno_z1ion, rep((peptide_height-len_annoSpace)*-1,
length(PSManno_z1ion)), col=y_ion_col, lwd=lwd)
segments(z1ion_xlarge, rep((peptide_height-len_annoSpace)*-1,
length(PSManno_z1ion)), PSManno_z1ion,
rep((peptide_height-len_annoSpace)*-1, length(PSManno_z1ion)),
col=y_ion_col, lwd=lwd)
text((z1ion_xlarge+PSManno_z1ion)/2,rep((peptide_height-len_annoSpace)*-1,
length(PSManno_z1ion)), PSManno_z1small, cex = 0.25, adj=c(0.5, -0.3),
col=y_ion_col)
}
}
}
# print identified peptide
print_modpeptide <- function(PSMlabel, peptide_height, mod_height,
pos_start_dash, pos_end_dash, direction){
#browser()
peptide_height <- peptide_height * direction
mod_height <- mod_height * direction
if (PSMlabel$peptide == ".") {
return(NULL)# ignore
} else if (grepl("^[A-Z]", PSMlabel$peptide) ||
PSMlabel$peptide == "-") {
# AA at the front
if (nchar(PSMlabel$peptide) == 1) {
# without modification
text( PSMlabel$AA_pos, peptide_height, PSMlabel$peptide,
cex = 0.5, adj = 0.5 )
} else{
# with modification at the end
AA <- substr(PSMlabel$peptide, 1, 1)
AA_endMod <-
substr(PSMlabel$peptide, 3, nchar(PSMlabel$peptide) - 1)
text( PSMlabel$AA_pos, peptide_height, bquote(.(AA)),
cex = 0.5, adj = 0.5 )
if (direction > 0) {
text( PSMlabel$AA_pos, peptide_height + mod_height,
bquote(""[.(AA_endMod)]), cex = 0.5, adj = 0.5 )
} else{
text( PSMlabel$AA_pos, peptide_height - mod_height,
bquote(""[.(AA_endMod)]), cex = 0.5, adj = 0.5 )
}
}
} else if (grepl("^\\(", PSMlabel$peptide)) {
# mod at the start
#browser()
bracket_start <- gregexpr("(", PSMlabel$peptide, fixed = TRUE)[[1]]
if (length(bracket_start) == 1) {
# only one mod which is at the start
AA_frontMod <-
substr(PSMlabel$peptide, 2, nchar(PSMlabel$peptide) - 2)
AA <- substring(PSMlabel$peptide, nchar(PSMlabel$peptide))
if (direction > 0) {
text( pos_start_dash, peptide_height + mod_height,
bquote(""[.(AA_frontMod)]), cex = 0.5, adj = 0.5 )
text( PSMlabel$AA_pos, peptide_height, bquote(.(AA)),
cex = 0.5, adj = 0.5 )
}else{
text( pos_start_dash, peptide_height - mod_height,
bquote(""[.(AA_frontMod)]), cex = 0.5, adj = 0.5 )
text(PSMlabel$AA_pos, peptide_height, bquote(.(AA)), cex = 0.5,
adj = 0.5 )
}
} else if (length(bracket_start) == 2) {
# two mod: one at the front and another at the end
AA_frontMod <- substr(PSMlabel$peptide, 2, bracket_start[2] - 3)
AA <-
substr(PSMlabel$peptide, bracket_start[2]-1, bracket_start[2]-1)
AA_endMod <-
substr(PSMlabel$peptide, bracket_start[2] + 1,
nchar(PSMlabel$peptide) - 1)
text(PSMlabel$AA_pos, peptide_height, bquote(.(AA)), cex = 0.5,
adj = 0.5)
if (direction > 0) {
text( pos_start_dash, peptide_height + mod_height,
bquote(""[.(AA_frontMod)]), cex = 0.5, adj = 0.5 )
text( PSMlabel$AA_pos, peptide_height + mod_height,
bquote(""[.(AA_endMod)]), cex = 0.5, adj = 0.5 )
} else{
text( pos_start_dash, peptide_height - mod_height,
bquote(""[.(AA_frontMod)]), cex = 0.5, adj = 0.5 )
text(PSMlabel$AA_pos,peptide_height - mod_height,
bquote(""[.(AA_endMod)]), cex = 0.5, adj = 0.5)
}
} else{
stop("CAN NOT BE THREE MODS! [note:stopped in print_modpeptide()].")
}
} else{
stop("CAN NOT BE THREE MODS! [note:stopped in print_modpeptide()].")
}
}
# write information about file, protein, MS2 retention time, charge and etc.
draw_ms2generalinfo<-function(rt, scan, mz, charge, gene, PSM, info_height){
direction <- PSM$direction[1]
rt <- paste("RT (min):", ifelse(rt<480, rt, round(rt/60, 1)))
scan <- paste("Scan:", scan)
mz <- paste("m/z:", round(mz, 2))
charge <- paste("Charge:", charge)
gene <- paste("Gene:", gene)
text(25, info_height*direction, paste(scan, mz, charge, rt, gene, sep="; "),
pos=4, offset=0, cex = 0.33)
}
# plot_group_individual
plot_group_individual<-function(mz_intensity_percent, AA_mz, PSM,
max_intensity, base_rawFile, rt, scan, mz, charge, gene, y_ion_col,
b_ion_col, peaks_col, ymax, lwd, peptide_height, mod_height, len_annoSpace,
srt, cex, max_mz, info_height, show_iontype){
#browser()
graphics::plot(mz_intensity_percent$mz, mz_intensity_percent$intensity_perc,
type = "h",las = 1, xlab = "", ylab = "", xlim = c(0, max_mz), xaxt="n",
yaxt="n", xaxs="i", yaxs="i", # w/o using axes=FALSE as want x/ylim
ylim = c(0, ymax), col = peaks_col, cex = cex, lwd=0.5,
frame.plot=FALSE) # max_intensity：1. give space of 0.7 for annotation
graphics::box(lwd=lwd/2)
label_axis(max_intensity, xlab="", ylab="", max_mz, cex, lwd)
# draw and color peak extension line
draw_peak_ionL(PSM, lwd, len_annoSpace, srt, show_iontype)
## draw PSM annotation (peptide, mod, b ions and y ions)
draw_psmanno( AA_mz, PSM, max_mz, peptide_height, mod_height, len_annoSpace,
y_ion_col, b_ion_col, lwd=lwd/2 )
## MS2 information ( file name, RT, Scan number, m/z, charge and gene name)
draw_ms2generalinfo( rt, scan, mz, charge, gene, PSM, info_height)
}
lileir/mms2plot documentation built on June 17, 2020, 9:16 a.m.
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Defines functions generate_ionLabel label_axis
# label x/y axis
label_axis<-function(max_intensity, xlab, ylab, max_mz, cex,lwd){
if(length(max_intensity) == 2){ # for mirror_plot
if( max_intensity[1] > 0){ # quarter of the max_intensity
axis_y_positive <- seq(0, max_intensity[1], length.out = 5)
axis_y_negative <- seq(max_intensity[2], 0, length.out = 5)
}else{# quarter of the max_intensity
axis_y_positive <- seq(max_intensity[1], 0, length.out = 5)
axis_y_negative <- seq(0, max_intensity[2], length.out = 5)
}
# remove duplicate "0" and keep 4 digits
axis_y <- signif(c(axis_y_negative, axis_y_positive[-1]), digits=4)
# abs( separate -1 to 1 with the length of 9 )
axis_y_percent <- scales::percent(abs(seq(-1, 1, length.out = 9)))
axis(side = 2,las = 1, at = seq(-1,1, length.out = 9),
labels = as.integer(axis_y), tck=-0.01, mgp=c(0, 0.2, 0),
cex.axis=0.33, lwd=0.5*lwd)
axis(side = 4,las = 1, at = seq(-1,1, length.out = 9),
labels = axis_y_percent, tck=-0.01, mgp=c(0, 0.2, 0),
cex.axis=0.33, lwd=0.5*lwd)
axis(side = 1, at=seq(0, max_mz, by=200), lwd=0.5*lwd, tck=-0.01,
labels=FALSE)
# mgp=c(0,0.1,0) NOT work for dist. betw. label and x-axis. mtext used.
graphics::mtext(side = 1, text=seq(0, max_mz, by=200),
at=seq(0, max_mz, by=200), cex=0.33*cex) #
}else{ # for group_plot
axis_y <- seq(0, max_intensity, length.out = 5)
axis_y_percent <- scales::percent(seq(0, 1, length.out = 5))
axis(side = 2,las = 1, at = seq(0, 1, length.out = 5),
labels = as.integer(axis_y), tck=-0.02, mgp=c(0, 0.2, 0),
cex.axis=0.33, lwd=0.5*lwd)
axis(side = 4,las = 1, at = seq(0, 1, length.out = 5),
labels = axis_y_percent, tck=-0.02, mgp=c(0, 0.2, 0),
cex.axis=0.33, lwd=0.5*lwd)
}
}
generate_ionLabel <- function(ionLabel_peak, show_iontype){
#browser()
# ionLabel_peaks_split = unlist(strsplit(ionLabel_peak), ",")
# for(i in 1:length(ionLabel_peaks_split)){
# ionLabel_peak = ionLabel_peaks_split[i]
# ion_name <- substr(ionLabel_peak, 1, regexpr(pattern ='\\+', ionLabel_peak)-1)
# number_plus <- substring(ionLabel_peak, regexpr(pattern ='\\+',ionLabel_peak))
# if(number_plus == "+"){number_plus = ""}
# else if(number_plus == "+*"){number_plus="*"}
# else if(number_plus == "++"){number_plus="2+"}
# else if(number_plus == "++*"){number_plus="2+*"}
#
# if(grepl("^z0", ion_name )){
# ion_number = substring(ion_name, 3)
# if(show_iontype){
# label = as.expression(bquote('z'^o*.(ion_number)^.(number_plus)))
# }else{
# label = as.expression(bquote(.(ion_number)^.(number_plus)))
# }
# }else{
# if(show_iontype){
# label = as.expression(bquote(.(ion_name)^.(number_plus)))
# }else{
# ion_name = substring(ion_name, 2)
# label = as.expression(bquote(.(ion_name)^.(number_plus)))
# }
# }
# }
show_iontype=T
# ionLabel_peak = "z08++,y7+"
# ionLabel_peak = "z08++"
ionLabel_peak = gsub("z0", "w", ionLabel_peak)
if(grepl(",", ionLabel_peak)){
ionLabel_peak = unlist(strsplit(ionLabel_peak, ","))
}
ionLabel <- substr(ionLabel_peak, 1, 1)
ionLabel_style <- ifelse(ionLabel == "w", "o", "")
ionLabel = gsub("w", "z", ionLabel)
ionLabel_number <- substr(ionLabel_peak, 2, regexpr(pattern ='\\+', ionLabel_peak)-1)
number_plus <- substring(ionLabel_peak, regexpr(pattern ='\\+',ionLabel_peak))
number_plus = gsub("^\\+\\+", "2+", number_plus)
number_plus = gsub("^\\+", "", number_plus)
if(length(ionLabel) == 1){
label = as.expression(bquote(.(ionLabel)^.(ionLabel_style)*.(ionLabel_number)^.(number_plus)))
}else if(length(ionLabel) == 2){
label = as.expression(bquote(paste(.(ionLabel[1])^.(ionLabel_style[1])*.(ionLabel_number[1])^.(number_plus[2]),",",.(ionLabel[2])^.(ionLabel_style[2])*.(ionLabel_number[2])^.(number_plus[2]),sep="")))
# label = as.expression(bquote(.(ionLabel[1])^.(ionLabel_style[1])*.(ionLabel_number[1])^.(number_plus[2]),.(ionLabel[2])^.(ionLabel_style[2])*.(ionLabel_number[2])^.(number_plus[2])))
}
# if(length(ionLabel_peak) == 1){
# if(grepl("^z0", ion_name )){
# ion_number = substring(ion_name, 3)
# if(show_iontype){
# label = as.expression(bquote('z'^o*.(ion_number)^.(number_plus)))
# }else{
# label = as.expression(bquote(.(ion_number)^.(number_plus)))
# }
# }else{
# if(show_iontype){
# label = as.expression(bquote(.(ion_name)^.(number_plus)))
# }else{
# ion_name = substring(ion_name, 2)
# label = as.expression(bquote(.(ion_name)^.(number_plus)))
# }
# }
# }
return(label)
}
# peaks annotation plot(rnorm(30), xlab = as.expression(bquote(.(a)^th*.(b))))
####################
draw_peak_ionL<-function(psm, lwd, len_annoSpace, srt,show_iontype){
#browser()
len_annoSpace = 0.05 # len_annoSpace / 2 distance between peak and label
ion_unique<-unique(psm, select=c("mz", "abs_intensity_prc_ext", "direction",
"intensity_perc","ionLabel_peak","col"))
lines(ion_unique$mz, ion_unique$intensity_perc, type = "h",las=1,
col=ion_unique$col, lwd = lwd/2)
segments(ion_unique$mz,ion_unique$intensity_perc, ion_unique$mz,
ion_unique$abs_intensity_prc_ext*ion_unique$direction,
col=ion_unique$col, lwd = lwd/2, lty=3) # draw peak extention segments
labels = mapply(generate_ionLabel, ion_unique$ionLabel_peak, show_iontype)
text( ion_unique$mz, (ion_unique$abs_intensity_prc_ext+len_annoSpace)
*ion_unique$direction,
labels <- labels, cex = 0.3, col=ion_unique$col,adj=0.5,srt=0)
#browser()
}
# generate and draw PSM labels
draw_psmanno<-function(AA_mz, PSM, max_mz, peptide_height, mod_height,
len_annoSpace, y_ion_col, b_ion_col, lwd){
#browser()
AA_mz = AA_mz[[1]] # change a list of data.frame to data.frame
# for peptide annotation, only consider aa with charge 1 for printing
AA_mz <- subset(AA_mz, AA_mz$charge == 1)
direction <- PSM$direction[1] # draw MS2 on upplot (1) or downplot (-1)
peptide <- c("-", as.character(AA_mz$aa_varmod), "-")
peptide_list <- vector("list", length(peptide)*2-1) # set peptide + two dash
peptide_list_b <- peptide_list # preset NULL for b ions
peptide_list_y <- peptide_list # preset NULL for y ions
peptide_list_c <- peptide_list # preset NULL for c ions
peptide_list_z0 <- peptide_list # preset NULL for z0 ions
peptide_list_z1 <- peptide_list # preset NULL for z1 ions
# set peptide
peptide_list[c(TRUE,FALSE)] <- as.list(peptide)
peptide_list[c(FALSE,TRUE)] <- as.list(".")
# set b ions
peptide_list_b[c(FALSE,TRUE)] <-
paste("b", seq(0,length(peptide)-2,by=1),sep="")
# set y ions
peptide_list_y[c(FALSE,TRUE)] <-
paste("y", rev(seq(0,length(peptide)-2,by=1)), sep="")
# set c ions
peptide_list_c[c(FALSE,TRUE)] <-
paste("c", seq(0,length(peptide)-2,by=1),sep="")
# set z ions
peptide_list_z0[c(FALSE,TRUE)] <-
paste("z0", rev(seq(0,length(peptide)-2,by=1)), sep="")
peptide_list_z1[c(FALSE,TRUE)] <-
paste("z'", rev(seq(0,length(peptide)-2,by=1)), sep="")
# set the width of AA sequence in the plot
x_quarter<-seq(0,max_mz, length.out = 20)[c(3,18)] # seq from 5/20 to 17/20
AA_pos <- seq(x_quarter[1], x_quarter[2], length.out=length(peptide_list))
pos_start_dash <- x_quarter[1] # x-axis value "-" at the front of peptides
pos_end_dash <- x_quarter[2] # x-axis value "-" at the end of peptides
# integrate as data.table
PSMlabel<-data.table::data.table(AA_pos=AA_pos, peptide=peptide_list,
bion=peptide_list_b, yion=peptide_list_y, cion = peptide_list_c,
z0ion = peptide_list_z0, z1ion = peptide_list_z1)
#browser()
apply(PSMlabel, 1, print_modpeptide, peptide_height, mod_height,
pos_start_dash, pos_end_dash, direction)# print AA letters for labelling
# draw b ions between AA letters
PSManno_bion <- subset(PSMlabel, PSMlabel$bion %in% PSM$ion)$AA_pos
index <- match(PSManno_bion,PSMlabel$AA_pos)-1
bion_xsmall <- (PSMlabel$AA_pos[index] + PSManno_bion)/2
PSManno_bsmall <-
substring(subset(PSMlabel, PSMlabel$bion %in% PSM$ion)$bion,2)
# draw y ions between AA letters
PSManno_yion <- subset(PSMlabel, PSMlabel$yion %in% PSM$ion)$AA_pos
index <- match(PSManno_yion,PSMlabel$AA_pos)+1
yion_xlarge <- (PSMlabel$AA_pos[index] + PSManno_yion)/2
PSManno_ysmall <-
substring(subset(PSMlabel, PSMlabel$yion %in% PSM$ion)$yion,2)
# draw c ions between AA letters
PSManno_cion <- subset(PSMlabel, PSMlabel$cion %in% PSM$ion)$AA_pos
index <- match(PSManno_cion,PSMlabel$AA_pos)-1
cion_xsmall <- (PSMlabel$AA_pos[index] + PSManno_cion)/2
PSManno_csmall <-
substring(subset(PSMlabel, PSMlabel$cion %in% PSM$ion)$cion,2)
# draw z0 ions between AA letters
PSManno_z0ion <- subset(PSMlabel, PSMlabel$z0ion %in% PSM$ion)$AA_pos
index <- match(PSManno_z0ion,PSMlabel$AA_pos)+1
z0ion_xlarge <- (PSMlabel$AA_pos[index] + PSManno_z0ion)/2
PSManno_z0small <-
substring(subset(PSMlabel, PSMlabel$z0ion %in% PSM$ion)$z0ion,3) # removing z'
# draw z1 ions between AA letters
PSManno_z1ion <- subset(PSMlabel, PSMlabel$z1ion %in% PSM$ion)$AA_pos
index <- match(PSManno_z1ion,PSMlabel$AA_pos)+1
z1ion_xlarge <- (PSMlabel$AA_pos[index] + PSManno_z1ion)/2
PSManno_z1small <-
substring(subset(PSMlabel, PSMlabel$z1ion %in% PSM$ion)$z1ion,3) # removing z'
#browser()
if(direction ==1){
if(length(PSManno_bion)>0){ # bion
segments(PSManno_bion, rep(peptide_height, length(PSManno_bion)),
PSManno_bion,rep(peptide_height-len_annoSpace,length(PSManno_bion)),
col=b_ion_col, lwd=lwd)
segments(bion_xsmall, rep(peptide_height-len_annoSpace,
length(PSManno_bion)), PSManno_bion,
rep(peptide_height-len_annoSpace, length(PSManno_bion)),
col=b_ion_col, lwd=lwd)
text((bion_xsmall+PSManno_bion)/2, rep(peptide_height-len_annoSpace,
length(PSManno_bion)), PSManno_bsmall, cex = 0.25, adj=c(0.5, 1.3),
col=b_ion_col)
}
if(length(PSManno_yion) > 0 ) { # y ion
segments(PSManno_yion, rep(peptide_height, length(PSManno_yion)),
PSManno_yion,rep(peptide_height+len_annoSpace,length(PSManno_yion)),
col=y_ion_col, lwd=lwd)
segments(yion_xlarge,
rep(peptide_height+len_annoSpace, length(PSManno_yion)),
PSManno_yion, rep(peptide_height+len_annoSpace,
length(PSManno_yion)), col=y_ion_col, lwd=lwd)
text((yion_xlarge+PSManno_yion)/2,
rep(peptide_height+len_annoSpace, length(PSManno_yion)),
PSManno_ysmall, cex = 0.25, adj=c(0.5, -0.3),col=y_ion_col)
}
if(length(PSManno_cion)>0){ # c ion
segments(PSManno_cion, rep(peptide_height, length(PSManno_cion)),
PSManno_cion,rep(peptide_height-len_annoSpace,length(PSManno_cion)),
col=b_ion_col, lwd=lwd)
segments(cion_xsmall, rep(peptide_height-len_annoSpace,
length(PSManno_cion)), PSManno_cion,
rep(peptide_height-len_annoSpace, length(PSManno_cion)),
col=b_ion_col, lwd=lwd)
text((cion_xsmall+PSManno_cion)/2, rep(peptide_height-len_annoSpace,
length(PSManno_cion)), PSManno_csmall, cex = 0.25, adj=c(0.5, 1.3),
col=b_ion_col)
}
if(length(PSManno_z0ion) > 0 ) { #z0 ion
segments(PSManno_z0ion, rep(peptide_height, length(PSManno_z0ion)),
PSManno_z0ion,rep(peptide_height+len_annoSpace,length(PSManno_z0ion)),
col=y_ion_col, lwd=lwd)
segments(z0ion_xlarge,
rep(peptide_height+len_annoSpace, length(PSManno_z0ion)),
PSManno_z0ion, rep(peptide_height+len_annoSpace,
length(PSManno_z0ion)), col=y_ion_col, lwd=lwd)
text((z0ion_xlarge+PSManno_z0ion)/2,
rep(peptide_height+len_annoSpace, length(PSManno_z0ion)),
PSManno_z0small, cex = 0.25, adj=c(0.5, -0.3),col=y_ion_col)
}
if(length(PSManno_z1ion) > 0 ) { # z1 ion
segments(PSManno_z1ion, rep(peptide_height, length(PSManno_z1ion)),
PSManno_z1ion,rep(peptide_height+len_annoSpace,length(PSManno_z1ion)),
col=y_ion_col, lwd=lwd)
segments(z1ion_xlarge,
rep(peptide_height+len_annoSpace, length(PSManno_z1ion)),
PSManno_z1ion, rep(peptide_height+len_annoSpace,
length(PSManno_z1ion)), col=y_ion_col, lwd=lwd)
text((z1ion_xlarge+PSManno_z1ion)/2,
rep(peptide_height+len_annoSpace, length(PSManno_z1ion)),
PSManno_z1small, cex = 0.25, adj=c(0.5, -0.3),col=y_ion_col)
}
}else{
if(length(PSManno_bion)>0){
segments(PSManno_bion, rep(peptide_height*-1, length(PSManno_bion)),
PSManno_bion,
rep((peptide_height+len_annoSpace)*-1, length(PSManno_bion)),
col=b_ion_col, lwd=lwd)
segments(bion_xsmall,
rep((peptide_height+len_annoSpace)*-1, length(PSManno_bion)),
PSManno_bion, rep((peptide_height+len_annoSpace)*-1,
length(PSManno_bion)), col=b_ion_col, lwd=lwd)
text((bion_xsmall+PSManno_bion)/2,rep((peptide_height+len_annoSpace)*-1,
length(PSManno_bion)), PSManno_bsmall, cex = 0.25, adj=c(0.5, 1.3),
col=b_ion_col)
}
if(length(PSManno_yion) > 0 ) {
segments(PSManno_yion, rep(peptide_height*-1, length(PSManno_yion)),
PSManno_yion, rep((peptide_height-len_annoSpace)*-1,
length(PSManno_yion)), col=y_ion_col, lwd=lwd)
segments(yion_xlarge, rep((peptide_height-len_annoSpace)*-1,
length(PSManno_yion)), PSManno_yion,
rep((peptide_height-len_annoSpace)*-1, length(PSManno_yion)),
col=y_ion_col, lwd=lwd)
text((yion_xlarge+PSManno_yion)/2,rep((peptide_height-len_annoSpace)*-1,
length(PSManno_yion)), PSManno_ysmall, cex = 0.25, adj=c(0.5, -0.3),
col=y_ion_col)
}
if(length(PSManno_cion)>0){
segments(PSManno_cion, rep(peptide_height*-1, length(PSManno_cion)),
PSManno_cion,
rep((peptide_height+len_annoSpace)*-1, length(PSManno_cion)),
col=b_ion_col, lwd=lwd)
segments(cion_xsmall,
rep((peptide_height+len_annoSpace)*-1, length(PSManno_cion)),
PSManno_cion, rep((peptide_height+len_annoSpace)*-1,
length(PSManno_cion)), col=b_ion_col, lwd=lwd)
text((cion_xsmall+PSManno_cion)/2,rep((peptide_height+len_annoSpace)*-1,
length(PSManno_cion)), PSManno_csmall, cex = 0.25, adj=c(0.5, 1.3),
col=b_ion_col)
}
if(length(PSManno_z0ion) > 0 ) {
segments(PSManno_z0ion, rep(peptide_height*-1, length(PSManno_z0ion)),
PSManno_z0ion, rep((peptide_height-len_annoSpace)*-1,
length(PSManno_z0ion)), col=y_ion_col, lwd=lwd)
segments(z0ion_xlarge, rep((peptide_height-len_annoSpace)*-1,
length(PSManno_z0ion)), PSManno_z0ion,
rep((peptide_height-len_annoSpace)*-1, length(PSManno_z0ion)),
col=y_ion_col, lwd=lwd)
text((z0ion_xlarge+PSManno_z0ion)/2,rep((peptide_height-len_annoSpace)*-1,
length(PSManno_z0ion)), PSManno_z0small, cex = 0.25, adj=c(0.5, -0.3),
col=y_ion_col)
}
if(length(PSManno_z1ion) > 0 ) {
segments(PSManno_z1ion, rep(peptide_height*-1, length(PSManno_z1ion)),
PSManno_z1ion, rep((peptide_height-len_annoSpace)*-1,
length(PSManno_z1ion)), col=y_ion_col, lwd=lwd)
segments(z1ion_xlarge, rep((peptide_height-len_annoSpace)*-1,
length(PSManno_z1ion)), PSManno_z1ion,
rep((peptide_height-len_annoSpace)*-1, length(PSManno_z1ion)),
col=y_ion_col, lwd=lwd)
text((z1ion_xlarge+PSManno_z1ion)/2,rep((peptide_height-len_annoSpace)*-1,
length(PSManno_z1ion)), PSManno_z1small, cex = 0.25, adj=c(0.5, -0.3),
col=y_ion_col)
}
}
}
# print identified peptide
print_modpeptide <- function(PSMlabel, peptide_height, mod_height,
pos_start_dash, pos_end_dash, direction){
#browser()
peptide_height <- peptide_height * direction
mod_height <- mod_height * direction
if (PSMlabel$peptide == ".") {
return(NULL)# ignore
} else if (grepl("^[A-Z]", PSMlabel$peptide) ||
PSMlabel$peptide == "-") {
# AA at the front
if (nchar(PSMlabel$peptide) == 1) {
# without modification
text( PSMlabel$AA_pos, peptide_height, PSMlabel$peptide,
cex = 0.5, adj = 0.5 )
} else{
# with modification at the end
AA <- substr(PSMlabel$peptide, 1, 1)
AA_endMod <-
substr(PSMlabel$peptide, 3, nchar(PSMlabel$peptide) - 1)
text( PSMlabel$AA_pos, peptide_height, bquote(.(AA)),
cex = 0.5, adj = 0.5 )
if (direction > 0) {
text( PSMlabel$AA_pos, peptide_height + mod_height,
bquote(""[.(AA_endMod)]), cex = 0.5, adj = 0.5 )
} else{
text( PSMlabel$AA_pos, peptide_height - mod_height,
bquote(""[.(AA_endMod)]), cex = 0.5, adj = 0.5 )
}
}
} else if (grepl("^\\(", PSMlabel$peptide)) {
# mod at the start
#browser()
bracket_start <- gregexpr("(", PSMlabel$peptide, fixed = TRUE)[[1]]
if (length(bracket_start) == 1) {
# only one mod which is at the start
AA_frontMod <-
substr(PSMlabel$peptide, 2, nchar(PSMlabel$peptide) - 2)
AA <- substring(PSMlabel$peptide, nchar(PSMlabel$peptide))
if (direction > 0) {
text( pos_start_dash, peptide_height + mod_height,
bquote(""[.(AA_frontMod)]), cex = 0.5, adj = 0.5 )
text( PSMlabel$AA_pos, peptide_height, bquote(.(AA)),
cex = 0.5, adj = 0.5 )
}else{
text( pos_start_dash, peptide_height - mod_height,
bquote(""[.(AA_frontMod)]), cex = 0.5, adj = 0.5 )
text(PSMlabel$AA_pos, peptide_height, bquote(.(AA)), cex = 0.5,
adj = 0.5 )
}
} else if (length(bracket_start) == 2) {
# two mod: one at the front and another at the end
AA_frontMod <- substr(PSMlabel$peptide, 2, bracket_start[2] - 3)
AA <-
substr(PSMlabel$peptide, bracket_start[2]-1, bracket_start[2]-1)
AA_endMod <-
substr(PSMlabel$peptide, bracket_start[2] + 1,
nchar(PSMlabel$peptide) - 1)
text(PSMlabel$AA_pos, peptide_height, bquote(.(AA)), cex = 0.5,
adj = 0.5)
if (direction > 0) {
text( pos_start_dash, peptide_height + mod_height,
bquote(""[.(AA_frontMod)]), cex = 0.5, adj = 0.5 )
text( PSMlabel$AA_pos, peptide_height + mod_height,
bquote(""[.(AA_endMod)]), cex = 0.5, adj = 0.5 )
} else{
text( pos_start_dash, peptide_height - mod_height,
bquote(""[.(AA_frontMod)]), cex = 0.5, adj = 0.5 )
text(PSMlabel$AA_pos,peptide_height - mod_height,
bquote(""[.(AA_endMod)]), cex = 0.5, adj = 0.5)
}
} else{
stop("CAN NOT BE THREE MODS! [note:stopped in print_modpeptide()].")
}
} else{
stop("CAN NOT BE THREE MODS! [note:stopped in print_modpeptide()].")
}
}
# write information about file, protein, MS2 retention time, charge and etc.
draw_ms2generalinfo<-function(rt, scan, mz, charge, gene, PSM, info_height){
direction <- PSM$direction[1]
rt <- paste("RT (min):", ifelse(rt<480, rt, round(rt/60, 1)))
scan <- paste("Scan:", scan)
mz <- paste("m/z:", round(mz, 2))
charge <- paste("Charge:", charge)
gene <- paste("Gene:", gene)
text(25, info_height*direction, paste(scan, mz, charge, rt, gene, sep="; "),
pos=4, offset=0, cex = 0.33)
}
# plot_group_individual
plot_group_individual<-function(mz_intensity_percent, AA_mz, PSM,
max_intensity, base_rawFile, rt, scan, mz, charge, gene, y_ion_col,
b_ion_col, peaks_col, ymax, lwd, peptide_height, mod_height, len_annoSpace,
srt, cex, max_mz, info_height, show_iontype){
#browser()
graphics::plot(mz_intensity_percent$mz, mz_intensity_percent$intensity_perc,
type = "h",las = 1, xlab = "", ylab = "", xlim = c(0, max_mz), xaxt="n",
yaxt="n", xaxs="i", yaxs="i", # w/o using axes=FALSE as want x/ylim
ylim = c(0, ymax), col = peaks_col, cex = cex, lwd=0.5,
frame.plot=FALSE) # max_intensity：1. give space of 0.7 for annotation
graphics::box(lwd=lwd/2)
label_axis(max_intensity, xlab="", ylab="", max_mz, cex, lwd)
# draw and color peak extension line
draw_peak_ionL(PSM, lwd, len_annoSpace, srt, show_iontype)
## draw PSM annotation (peptide, mod, b ions and y ions)
draw_psmanno( AA_mz, PSM, max_mz, peptide_height, mod_height, len_annoSpace,
y_ion_col, b_ion_col, lwd=lwd/2 )
## MS2 information ( file name, RT, Scan number, m/z, charge and gene name)
draw_ms2generalinfo( rt, scan, mz, charge, gene, PSM, info_height)
}
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