Created
January 23, 2020 16:21
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Drosophila Model
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library(ggplot2) | |
library(deSolve) | |
library(ggpubr) | |
'%=%' <- function(x, y) { | |
x <- as.character(substitute(x)[-1]) | |
if (length(y) < length(x)) | |
y <- rep(y, ceiling(length(x) / length(y))) | |
if (length(y) > length(x)) | |
y <- y[1:length(x)] | |
mapply(assign, x, y, MoreArgs = list(envir = parent.frame())) | |
invisible() | |
} | |
h <- function(v) v > 0 | |
dt_x <- 0 | |
dt_y <- 0 | |
dt_z <- 0 | |
dt_u <- 0 | |
dt_w <- 0 | |
dt_p <- 0 | |
Gro <- 1 | |
EMC <- 1 | |
D <- 2.05 | |
L <- 1 | |
UB <- 1.17 | |
SINA <- 5.6 | |
C <- 1 | |
n1 <- 2 | |
n3 <- 2 | |
n5 <- 2 | |
m1 <- 1.77 | |
m2 <- 1 | |
m3 <- 1 | |
m4 <- 1 | |
m5 <- 1 | |
m6 <- 1 | |
m7 <- 1 | |
kx <- 1 | |
ky <- 1 | |
kz <- 1 | |
ku <- 1 | |
kw <- 1 | |
kp <- 1 | |
a3 <- 3.61 | |
b3 <- 4.96 | |
c3 <- 1.35 | |
a4 <- 4.43 | |
b4 <- 6.09 | |
c4 <- 1.66 | |
a5 <- 8.09 | |
b5 <- 11.13 | |
c5 <- 3.03 | |
a6 <- 2.67 | |
b6 <- 3.67 | |
c6 <- 1 | |
d1 <- 7.46 | |
d3 <- 2.77 | |
d5 <- 1.24 | |
x0 <- 0.56 | |
y0 <- 1.59 | |
z0 <- 0.15 | |
u0 <- 0 | |
w0 <- 0 | |
p0 <- 0 | |
sigma1 <- function (v) { | |
h(v) * d1 * v ^ n1 / (1 + v ^ n1) | |
} | |
sigma3 <- function (v) { | |
h(v) * d3 * v ^ n3 / (1 + v ^ n3) | |
} | |
sigma5 <- function (v) { | |
h(v) * d5 * v ^ n5 / (1 + v ^ n5) | |
} | |
s3 <- function (v) { | |
h(v) * a3 * exp((v - b3) / c3) / (1 + exp((v - b3) / c3)) | |
} | |
s4 <- function (v) { | |
h(v) * a4 * exp((v - b4) / c4) / (1 + exp((v - b4) / c4)) | |
} | |
s5 <- function (v) { | |
h(v) * a5 * exp((v - b5) / c5) / (1 + exp((v - b5) / c5)) | |
} | |
s6 <- function (v) { | |
h(v) * a6 * exp((v - b6) / c6) / (1 + exp((v - b6) / c6)) | |
} | |
# Helper for x' | |
x_helper <- function(t, lagPoint, currentPoint = lagPoint) { | |
c(x, y, z, u, w, p) %=% lagPoint | |
c(x_curr, y_curr, z_curr, u_curr, w_curr, p_curr) %=% currentPoint | |
kx * (sigma1(D * x) + sigma3(z) + sigma5(w)) / ((1 + Gro * y) * (1 + EMC * x)) - m1 * x * (1 + p_curr * UB * SINA) | |
} | |
# Modelling for x' | |
x_model <- function(t, dt, startValue, point, args, ...) { | |
if (t < 0) { startValue } | |
else if (t < dt || dt < 0.01) { | |
lagPoint <- x_helper(t, point) | |
} else { | |
lagPoint <- lagvalue(t - dt) | |
x_helper(t, lagPoint, point) | |
} | |
} | |
# Helper for y' | |
y_helper <- function(t, lagPoint, currentPoint = lagPoint) { | |
c(x, y, z, u, w, p) %=% lagPoint | |
c(x_curr, y_curr, z_curr, u_curr, w_curr, p_curr) %=% currentPoint | |
ky * C / (1 + u ^ m7) - m2 * y_curr | |
} | |
# Modelling for y' | |
y_model <- function(t, dt, startValue, point, args, ...) { | |
if (t < 0) { startValue } | |
else if (t < dt || dt < 0.01) { | |
lagPoint <- y_helper(t, point) | |
} else { | |
lagPoint <- lagvalue(t - dt) | |
y_helper(t, lagPoint, point) | |
} | |
} | |
# Helper for z' | |
z_helper <- function(t, lagPoint, currentPoint = lagPoint) { | |
c(x, y, z, u, w, p) %=% lagPoint | |
c(x_curr, y_curr, z_curr, u_curr, w_curr, p_curr) %=% currentPoint | |
kz * s3(D * x) - m3 * z_curr | |
} | |
# Modelling for z' | |
z_model <- function(t, dt, startValue, point, args, ...) { | |
if (t < 0) { startValue } | |
else if (t < dt || dt < 0.01) { | |
lagPoint <- z_helper(t, point) | |
} else { | |
lagPoint <- lagvalue(t - dt) | |
z_helper(t, lagPoint, point) | |
} | |
} | |
# Helper for u' | |
u_helper <- function(t, lagPoint, currentPoint = lagPoint) { | |
c(x, y, z, u, w, p) %=% lagPoint | |
c(x_curr, y_curr, z_curr, u_curr, w_curr, p_curr) %=% currentPoint | |
ku * s4(D * x) - m4 * u_curr | |
} | |
# Modelling for u' | |
u_model <- function(t, dt, startValue, point, args, ...) { | |
if (t < 0) { startValue } | |
else if (t < dt || dt < 0.01) { | |
lagPoint <- u_helper(t, point) | |
} else { | |
lagPoint <- lagvalue(t - dt) | |
u_helper(t, lagPoint, point) | |
} | |
} | |
# Helper for w' | |
w_helper <- function(t, lagPoint, currentPoint = lagPoint) { | |
c(x, y, z, u, w, p) %=% lagPoint | |
c(x_curr, y_curr, z_curr, u_curr, w_curr, p_curr) %=% currentPoint | |
kw * s5(D * x) - m5 * w_curr | |
} | |
# Modelling for w' | |
w_model <- function(t, dt, startValue, point, args, ...) { | |
if (t < 0) { startValue } | |
else if (t < dt || dt < 0.01) { | |
lagPoint <- w_helper(t, point) | |
} else { | |
lagPoint <- lagvalue(t - dt) | |
w_helper(t, lagPoint, point) | |
} | |
} | |
# Helper for p' | |
p_helper <- function(t, lagPoint, currentPoint = lagPoint) { | |
c(x, y, z, u, w, p) %=% lagPoint | |
c(x_curr, y_curr, z_curr, u_curr, w_curr, p_curr) %=% currentPoint | |
h(t - 12) * (kp * s6(D * x) * (t - 12) ^ 2 / (L + (t - 12) ^ 2) - m6 * p_curr) | |
} | |
# Modelling for p' | |
p_model <- function(t, dt, startValue, point, args, ...) { | |
if (t < 0) { startValue } | |
else if (t < dt || dt < 0.01) { | |
lagPoint <- p_helper(t, point) | |
} else { | |
lagPoint <- lagvalue(t - dt) | |
p_helper(t, lagPoint, point) | |
} | |
} | |
# Modelling stuff | |
simulate <- function() { | |
model <- function(t, p, parms, ...) { | |
list(c(x_model(t, dt_x, x0, p), y_model(t, dt_y, y0, p), z_model(t, dt_z, z0, p), u_model(t, dt_u, u0, p), w_model(t, dt_w, w0, p), p_model(t, dt_p, p0, p))) | |
} | |
t <- seq(0, 16, by = 0.1) | |
start <- c(x0 * kx, y0 * ky, z0 * kz, u0 * ku, w0 * kw, p0 * kp) | |
traj <- as.data.frame(dede(start, t, func = model)) | |
plot_x <- traj[, 2] | |
plot_y <- traj[, 3] | |
plot_z <- traj[, 4] | |
plot_u <- traj[, 5] | |
plot_w <- traj[, 6] | |
plot_p <- traj[, 7] | |
linetypes <- c("solid", "dashed", "dotted") | |
df <- rbind( | |
data.frame(t, value = plot_x, side = 1, f = "AS-C: x(t)"), | |
data.frame(t, value = plot_y, side = 1, f = "Hairy: y(t)"), | |
data.frame(t, value = plot_z, side = 1, f = "Senseless: z(t)"), | |
data.frame(t, value = plot_u, side = 2, f = "Scratch: u(t)"), | |
data.frame(t, value = plot_w, side = 2, f = "Charlatan: w(t)"), | |
data.frame(t, value = plot_p, side = 2, f = "Phyllopod: p(t)") | |
) | |
return(df) | |
} | |
draw_plot_small <- function(df, side) { | |
ggplot(df[df$side == side, ], aes(x = t, y = value, color = f, group = f)) + | |
geom_line(aes(linetype = f)) + | |
ylim(0, max(df$value)) + | |
ylab("") + | |
scale_linetype_manual(values = c("solid", "longdash", "dotdash")) + | |
theme_bw()+ | |
theme(legend.position = "none") | |
} | |
draw_plot_big <- function(df, filename) { | |
p1 <- draw_plot_small(df, 1) | |
p2 <- draw_plot_small(df, 2) | |
p <- ggarrange(p1, p2) | |
ggsave(paste0(filename, ".png"), p, dpi = 1200, width = 6, height = 4) | |
show(p) | |
} | |
simulate_and_draw <- function(filename, kx.value) { | |
kx <<- kx.value | |
df <- simulate() | |
draw_plot_big(df, filename) | |
} | |
simulate_and_draw("figure2", 1) | |
simulate_and_draw("figure3", 0.8) | |
simulate_and_draw("figure4", 0.66) | |
simulate_and_draw("figure5", 0.65) | |
simulate_and_draw("figure6", 0.6) |
Author
AndreyAkinshin
commented
Jan 23, 2020
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