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#import "@preview/lilaq:0.3.0" as lq
#import "@preview/tiptoe:0.3.0"
#let ion-colors = (
y: color.red,
b: color.blue,
yp: color.red,
ystar: color.red,
"y*": color.red,
yO: color.orange,
x: color.orange,
bstar: color.blue,
"b*": color.blue,
bO: rgb("#ff00ff"),
a: color.green,
astar: color.green,
aO: color.green,
c: color.blue,
z: color.red,
bp: color.blue
)
#let psm-ionlabel(name, size, charge) = [
#let str_charge = ("", "+", "++", "+++")
$#name _#size^#str_charge.at(charge)$
]
#let ms2spectra-delta-diagram = it => {
show: lq.set-diagram(
xlabel: [$m/z$],
ylabel: [Mass delta (ppm)],
legend: none,
grid: none,
xaxis: (mirror: none),
yaxis: (mirror: none),
)
it
}
#let ms2spectra-diagram = it => {
show: lq.set-diagram(
xlabel: [$m/z$],
ylabel: [Intensity],
legend: none,
grid: none,
xaxis: (mirror: none),
yaxis: (mirror: none),
)
it
}
#let ms2spectra-simple-plot(spectra) = {
lq.stem(spectra.mz, spectra.intensity,
color: black,
base-stroke : none,
mark: none)
}
#let ms2spectra-ion-plot(type, ion_arr) = {
let mz_arr = ()
let int_arr = ()
for one_ion in ion_arr {
mz_arr.push(one_ion.mz)
int_arr.push(one_ion.intensity)
}
(
lq.stem(mz_arr, int_arr, stroke: 1.1pt, base-stroke : none, color: ion-colors.at(type), mark:none, label: [#type])
,
ion_arr.map((one_ion) => {
let display = true
if(("isotope" in one_ion)) {
if (one_ion.isotope != 0) {
display = false
}
}
if(display) {
let align = bottom
lq.place(clip: true, one_ion.mz, one_ion.intensity, pad(bottom: 0.3em, left: 20%)[#text(ion-colors.at(type), size: 8pt)[#psm-ionlabel(type,one_ion.size, one_ion.charge)]], align: align)
}
})
)
}
#let ms2spectra-delta-plot(delta_arr) = {
delta_arr.map((delta) => {
let level = 1em * delta.level + 1em
(
lq.line(
tip: tiptoe.bar,
toe: tiptoe.bar,
stroke: (paint: ion-colors.at(delta.ion)),
(delta.mz.at(0), level), (delta.mz.at(1), level)),
lq.place(clip: true, (delta.mz.at(1)+delta.mz.at(0))/2, level,
pad(bottom: 0.8em)[#text(ion-colors.at(delta.ion), size: 8pt)[#delta.label]]
)
)
})
}
#let xic-plot(
title: none,
rt_range: auto,
max_intensity: none,
..xic_json_list
) = {
let ylimit = auto;
if (max_intensity != none) {ylimit = (0, max_intensity)}
lq.diagram(
title: title,
xlabel: [Retention time (s)],
ylabel: [Intensity],
ylim: ylimit,
xlim: rt_range,
..xic_json_list.pos().map((one_xic) => {
let label = none
if ("title" in one_xic) {label = one_xic.title}
lq.plot(one_xic.x, one_xic.y, label: label)
})
)
}
#let ms2spectra-ion-delta-plot(type, ion_arr) = {
let one_million = 1000000
let mz_arr = ()
let mz_delta_arr = ()
for one_ion in ion_arr {
mz_arr.push(one_ion.mz)
mz_delta_arr.push((one_ion.mz - one_ion.mzth) / (one_ion.mz / one_million))
}
lq.scatter(mz_arr, mz_delta_arr, color: ion-colors.at(type))
}
#let ms2spectra-plot(
title: none,
mz_range: none,
max_intensity: none,
spectra: none,
ion-series: none,
delta: none,
delta-fragments: false,
psm_json_data
) = {
let ylimit = auto;
if (max_intensity != none) {ylimit = (0, max_intensity)}
if(("delta" in psm_json_data)) {
delta = psm_json_data.delta
}
if(("spectra" in psm_json_data)) {
spectra = psm_json_data.spectra
}
if(("ion-series" in psm_json_data)) {
ion-series = psm_json_data.ion-series
}
let mzpc = (spectra.mz.last() - spectra.mz.first()) / 100
let inside_xlim = (spectra.mz.first()- 2*mzpc, spectra.mz.last()+ 2*mzpc)
if (mz_range != none) {inside_xlim = mz_range}
show: ms2spectra-diagram
lq.diagram(
title: title,
xlim: inside_xlim,
ylim: ylimit,
if((spectra != none)) {ms2spectra-simple-plot(spectra)},
..if((ion-series != none)) {ion-series.pairs().map(((type, ion_arr)) => {
ms2spectra-ion-plot(type, ion_arr)
}).flatten()},
..if((delta != none)) {ms2spectra-delta-plot(delta).flatten()},
if(delta-fragments) {
lq.place(
100%, 100%+2em,
align: right+top,
lq.diagram(
height: 1.5cm,
margin: 0%,
ylabel: [delta ppm],
ylim: (-10, 10),
xlim: inside_xlim,
xaxis: none,
..if((ion-series != none)) {ion-series.pairs().map(((type, ion_arr)) => {
ms2spectra-ion-delta-plot(type, ion_arr)
}).flatten()},
lq.line(stroke: (paint: blue, dash: "dashed"),(0, 0), ( 100%,0))
)
)}
)
}
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