Created
May 7, 2020 10:34
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install.packages(c('data.table','IsoSpecR','ggplot2','ggthemes')) | |
library(data.table) | |
library(IsoSpecR) | |
library(ggplot2) | |
library(ggthemes) | |
isoDist = function(mol, P=.99, ...) as.data.table(IsoSpecify(molecule=mol, P, showCounts=1,...)) | |
marginal = function(mol, cutoff, space=0) isoDist(mol, cutoff, algo=3)[order(prob, decreasing=TRUE)][,rprob:=prob/prob[1]][,R:=cumsum(rprob) + (0:(nrow(.SD)-1))*space][,L:=R-rprob ] | |
get_R = function(mol=c(C=1000,H=2002), P=.999, space=0){ | |
R = isoDist(mol, P) | |
R = R[order(prob, decreasing = TRUE)] | |
maxIso = R[which.max(prob)] # top isotopologue | |
maxIsoP = maxIso$prob | |
minCisoP = R[C12==maxIso$C12][which.min(prob)]$prob # min-prob-isotopologue on the C axis | |
minCsubisoRatio = minCisoP/maxIsoP/2 # 2 just to be sure | |
minHisoP = R[H1==maxIso$H1][which.min(prob)]$prob # min-prob-isotopologue on the H axis | |
minHsubisoRatio = minHisoP/maxIsoP/2 # 2 just to be sure | |
C = marginal(mol['C'], minCsubisoRatio, space) | |
H = marginal(mol['H'], minHsubisoRatio, space) | |
R = merge(R, C, by=c('C12','C13'), suffixes=c('','.C')) | |
R = merge(R, H, by=c('H1','H2'), suffixes=c('','.H')) | |
setnames(R, c('rprob','R','L'), c('rprob.C','R.C','L.C')) | |
R = R[order(prob, decreasing = T)] | |
R | |
} | |
mol = c(C=1000, H=2002)*100 | |
P = .999 | |
R = get_R(mol, P) | |
# R = get_R(c(C=10000,H=20002), .999, .1) | |
R$col = c(rep('red', 500), rep('orange', 500), rep('yellow', 500), rep('darkblue', nrow(R)-500*3)) | |
ggplot(R) + | |
geom_rect(aes(xmin=L.C, xmax=R.C, ymin=L.H, ymax=R.H, fill=I(col)), color='black') + | |
theme_tufte() + | |
theme(axis.title=element_blank(), | |
axis.text=element_blank(), | |
axis.ticks=element_blank()) |
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