Nothing
### This is for simulation only, ploting delta.t * phi aganst true values.
plot.aa.allinone <- function(
i.aa, id.label, tl.codon, ### For AA.
label.negsel.true, ### For label.
b.Init, EPhi, ### For true.
b.mcmc, t.phi.mcmc, ### For unscaled results.
b.negsel.PM, phi.PM, ### For scaled results.
workflow.name, i.case, model){
### Get right b for AA.
b.AA.true <- b.Init[id.label]
b.AA.PM <- matrix(b.mcmc[id.label,], nrow = tl.codon)
b.AA.PM.scaled <- b.negsel.PM[id.label]
### Get true deltat * phi
deltat.phi.true <- NULL
for(i.codon in 1:tl.codon){
deltat.phi.true <- cbind(deltat.phi.true,
b.AA.true[i.codon] * EPhi)
}
### Get mean of unscaled deltat * phi
deltat.phi.PM <- NULL
for(i.codon in 1:tl.codon){
deltat.phi.PM <- cbind(deltat.phi.PM,
colMeans(b.AA.PM[i.codon,] * t.phi.mcmc))
}
### Get scaled deltat * scaled phi
deltat.phi.PM.scaled <- NULL
for(i.codon in 1:tl.codon){
deltat.phi.PM.scaled <- cbind(deltat.phi.PM.scaled,
b.AA.PM.scaled[i.codon] * phi.PM)
}
### AA plot.
# nf <- layout(matrix(1:3, nrow = 3), 1, c(1, 4, 4), respect = FALSE)
### Plot title.
# par(mar = c(0, 0, 0, 0))
# plot(NULL, NULL, xlim = c(0, 1), ylim = c(0, 1), axes = FALSE)
# text(0.5, 0.5,
# paste(workflow.name, ", ", get.case.main(i.case, model), sep = ""))
# par(mar = c(5.1, 4.1, 4.1, 2.1))
### Plot codon with large range first.
diff.range <- apply(deltat.phi.true, 2, function(x){ abs(diff(range(x))) })
order.plot <- order(diff.range, decreasing = TRUE)
u.codon <- gsub(".\\.(.*)", "\\1", label.negsel.true[id.label])
u.codon.sorted <- sort(u.codon)
color <- cubfits:::get.color(u.codon.sorted)
### Plot top row.
lim <- range(range(deltat.phi.true), range(deltat.phi.PM))
plot(NULL, NULL,
xlim = lim, ylim = lim,
xlab = "true Delta.t * true Phi", ylab = "mean (Delta.t * Phi)",
main = i.aa)
for(i.codon in order.plot){
points(deltat.phi.true[, i.codon], deltat.phi.PM[, i.codon],
col = color[u.codon.sorted == u.codon[i.codon]],
pch = 20, cex = 0.5)
}
abline(a = 0, b = 1, col = 4, lty = 2)
# legend(lim[2] + (lim[2] - lim[1]) * (-0.3),
# lim[2] - (lim[2] - lim[1]) * 0.8,
# "1-to-1", col = 4, lty = 2)
### Plot bottom row.
# lim <- range(range(deltat.phi.true), range(deltat.phi.PM.scaled))
# plot(NULL, NULL,
# xlim = lim, ylim = lim,
# xlab = "true Delta.t * true Phi",
# ylab = "mean scaled Delta.t * mean scaled Phi",
# main = i.aa)
# for(i.codon in order.plot){
# points(deltat.phi.true[, i.codon], deltat.phi.PM.scaled[, i.codon],
# col = color[u.codon.sorted == u.codon[i.codon]],
# pch = 20, cex = 0.5)
# }
# abline(a = 0, b = 1, col = 4, lty = 2)
# legend(lim[2] + (lim[2] - lim[1]) * (-0.3),
# lim[2] - (lim[2] - lim[1]) * 0.8,
# "1-to-1", col = 4, lty = 2)
invisible()
} # End of plot.aa.allinone().
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