RNA kinetics

kinetics.R

library(deSolve)
library(ggplot2)

RNAvelo <- function(Time, State, Pars, input) {
  with(as.list(c(State, Pars)), {
    import <- input(Time)
    du   <- import  - beta * U
    ds   <- beta * U - gamma * S
    return(list(c(du, ds)))
  })
}

parms <- c(beta = 0.1, gamma = 0.05)
times <- seq(0, 100, length = 101)
signal <- data.frame(times = times,
                     import = rep(0, length(times)))
signal$import[signal$times <= 11] <- 0.1

sigimp <- approxfun(signal$times, signal$import, rule = 2)
curve(sigimp(x), 0, 100)

xstart <- c(U=0, S = 0)
out <- ode(y = xstart, times = times,
           func = RNAvelo, parms = parms, input = sigimp)

dfout <- as.data.frame(out)

ggplot(dfout, aes(x=time))+
  geom_line(aes(y=U, colour="U"))+
  geom_line(aes(y=S, colour="S"))+
  labs(colour="")+
  geom_vline(xintercept = 11, linetype=2)+
  theme_bw(15)

ggsave("time_SU.png")

ggplot(dfout, aes(x=S,y=U))+
  geom_path()+
  geom_point(aes(colour=time))+
  theme_bw(15)

ggsave("SvsU.png")